aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--.travis.yml8
-rw-r--r--dev-python/hdf5storage/Manifest1
-rw-r--r--dev-python/hdf5storage/hdf5storage-0.1.13.ebuild22
-rw-r--r--dev-python/matplotlib2tikz/Manifest1
-rw-r--r--dev-python/matplotlib2tikz/matplotlib2tikz-0.5.6.ebuild24
-rw-r--r--sci-biology/CONTIGuator/CONTIGuator-2.7.3.ebuild31
-rw-r--r--sci-biology/CONTIGuator/CONTIGuator-2.7.ebuild17
-rw-r--r--sci-biology/CONTIGuator/Manifest1
-rw-r--r--sci-biology/DisEMBL/DisEMBL-1.4.ebuild2
-rw-r--r--sci-biology/MolBioLib/Manifest1
-rw-r--r--sci-biology/MolBioLib/MolBioLib-5.ebuild31
-rw-r--r--sci-biology/MolBioLib/metadata.xml (renamed from sci-biology/abyss/metadata.xml)4
-rw-r--r--sci-biology/ONTO-PERL/ONTO-PERL-1.41.ebuild6
-rw-r--r--sci-biology/TransDecoder/Manifest1
-rw-r--r--sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild83
-rw-r--r--sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch22
-rw-r--r--sci-biology/abyss/Manifest3
-rw-r--r--sci-biology/abyss/abyss-1.3.3-r1.ebuild42
-rw-r--r--sci-biology/abyss/abyss-1.3.4-r1.ebuild47
-rw-r--r--sci-biology/abyss/abyss-1.3.6-r1.ebuild48
-rw-r--r--sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch18
-rw-r--r--sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch15
-rw-r--r--sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch40
-rw-r--r--sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch15
-rw-r--r--sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch40
-rw-r--r--sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch18
-rw-r--r--sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch15
-rw-r--r--sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch40
-rw-r--r--sci-biology/act-bin/Manifest4
-rw-r--r--sci-biology/act-bin/act-bin-13.0.0.ebuild50
-rw-r--r--sci-biology/act-bin/metadata.xml12
-rw-r--r--sci-biology/amos/amos-3.1.0-r2.ebuild9
-rw-r--r--sci-biology/amos/amos-9999.ebuild10
-rw-r--r--sci-biology/arachne/Manifest1
-rw-r--r--sci-biology/arachne/arachne-46233.ebuild41
-rw-r--r--sci-biology/arachne/metadata.xml12
-rw-r--r--sci-biology/artemis-bin/Manifest4
-rw-r--r--sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild29
-rw-r--r--sci-biology/artemis/Manifest3
-rw-r--r--sci-biology/artemis/artemis-9999.ebuild19
-rw-r--r--sci-biology/bamtools/Manifest1
-rw-r--r--sci-biology/bamtools/bamtools-2.4.0.ebuild31
-rw-r--r--sci-biology/bamtools/files/bamtools-2.4.0-unbundle.patch23
-rw-r--r--sci-biology/cap3-bin/Manifest1
-rw-r--r--sci-biology/cap3-bin/cap3-bin-20071015.ebuild (renamed from sci-biology/cap3-bin/cap3-bin-20071221.ebuild)0
-rw-r--r--sci-biology/cap3-bin/cap3-bin-20150210.ebuild42
-rw-r--r--sci-biology/cd-hit/Manifest2
-rw-r--r--sci-biology/cd-hit/cd-hit-4.6.1.ebuild44
-rw-r--r--sci-biology/cd-hit/cd-hit-4.6.5.ebuild61
-rw-r--r--sci-biology/cd-hit/files/4.6.5-gentoo.patch (renamed from sci-biology/cd-hit/files/4.6.1-gentoo.patch)95
-rw-r--r--sci-biology/cd-hit/files/cd-hit-auxtools-manual.txt212
-rw-r--r--sci-biology/cg-cat/cg-cat-20150130.ebuild35
-rw-r--r--sci-biology/consed/consed-29.ebuild12
-rw-r--r--sci-biology/cross_genome/cross_genome-20140822.ebuild2
-rw-r--r--sci-biology/cutadapt/Manifest4
-rw-r--r--sci-biology/cutadapt/cutadapt-1.4.1.ebuild18
-rw-r--r--sci-biology/cutadapt/cutadapt-1.5.ebuild18
-rw-r--r--sci-biology/cutadapt/cutadapt-1.9.1.ebuild (renamed from sci-biology/cutadapt/cutadapt-1.2.1.ebuild)2
-rw-r--r--sci-biology/cutadapt/cutadapt-9999.ebuild2
-rw-r--r--sci-biology/exomiser-bin/Manifest4
-rw-r--r--sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild23
-rw-r--r--sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild31
-rw-r--r--sci-biology/fgap-bin/Manifest1
-rw-r--r--sci-biology/fgap-bin/fgap-bin-1.8.1.ebuild25
-rw-r--r--sci-biology/fgap-bin/metadata.xml12
-rw-r--r--sci-biology/fgap/Manifest1
-rw-r--r--sci-biology/fgap/fgap-1.8.1.ebuild26
-rw-r--r--sci-biology/fgap/metadata.xml12
-rw-r--r--sci-biology/fsl/fsl-5.0.8.ebuild2
-rw-r--r--sci-biology/gap2caf/gap2caf-2.1.0.ebuild4
-rw-r--r--sci-biology/karect/Manifest1
-rw-r--r--sci-biology/karect/karect-1.0.0.ebuild33
-rw-r--r--sci-biology/karect/metadata.xml12
-rw-r--r--sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild6
-rw-r--r--sci-biology/perga/metadata.xml12
-rw-r--r--sci-biology/perga/perga-9999.ebuild36
-rw-r--r--sci-biology/perlprimer/perlprimer-1.1.21.ebuild2
-rw-r--r--sci-biology/reapr/Manifest2
-rw-r--r--sci-biology/reapr/files/fix_sort_samtools13.patch16
-rw-r--r--sci-biology/reapr/files/use_shared_libs.patch252
-rw-r--r--sci-biology/reapr/metadata.xml12
-rw-r--r--sci-biology/reapr/reapr-1.0.18.ebuild62
-rw-r--r--sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild6
-rw-r--r--sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild2
-rw-r--r--sci-biology/scbi_mapreduce/Manifest2
-rw-r--r--sci-biology/scbi_mapreduce/scbi_mapreduce-0.0.45.ebuild (renamed from sci-biology/scbi_mapreduce/scbi_mapreduce-0.0.40.ebuild)2
-rw-r--r--sci-biology/scythe/scythe-0.992.ebuild2
-rw-r--r--sci-biology/staden/Manifest3
-rw-r--r--sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch (renamed from sci-biology/staden/files/staden-2.0.0_beta9-ldflags.patch)0
-rw-r--r--sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch (renamed from sci-biology/staden/files/staden-2.0.0_beta9-zlib.patch)0
-rw-r--r--sci-biology/staden/files/staden-2.0.0_beta9-libpng-1.5.patch16
-rw-r--r--sci-biology/staden/staden-2.0.0_beta10.ebuild (renamed from sci-biology/staden/staden-2.0.0_beta9.ebuild)31
-rw-r--r--sci-biology/staden/staden-9999.ebuild19
-rw-r--r--sci-biology/staden_doc/Manifest1
-rw-r--r--sci-biology/staden_doc/metadata.xml12
-rw-r--r--sci-biology/staden_doc/staden_doc-2.0.0_beta9.ebuild44
-rw-r--r--sci-biology/trimmomatic/Manifest4
-rw-r--r--sci-biology/trimmomatic/trimmomatic-0.35.ebuild (renamed from sci-biology/trimmomatic/trimmomatic-0.32.ebuild)2
-rw-r--r--sci-chemistry/nwchem/Manifest14
-rw-r--r--sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch12
-rw-r--r--sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild4
-rw-r--r--sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild279
-rw-r--r--sci-libs/armadillo/Manifest3
-rw-r--r--sci-libs/armadillo/armadillo-6.200.5.ebuild (renamed from sci-libs/armadillo/armadillo-6.200.3.ebuild)0
-rw-r--r--sci-libs/armadillo/armadillo-6.600.5.ebuild121
-rw-r--r--sci-libs/calculix-ccx/Manifest6
-rw-r--r--sci-libs/calculix-ccx/calculix-ccx-2.10.ebuild (renamed from sci-libs/calculix-ccx/calculix-ccx-2.8_p2.ebuild)15
-rw-r--r--sci-libs/calculix-ccx/files/01_ccx_2.10_Makefile_custom_cc_flags_spooles_arpack.patch35
-rw-r--r--sci-libs/calculix-ccx/files/01_ccx_2.7_Makefile_custom_cc_flags_spooles_arpack.patch31
-rw-r--r--sci-libs/calculix-ccx/files/01_ccx_2.7_lapack.patch11
-rw-r--r--sci-libs/calculix-ccx/files/01_ccx_2.8p2_Makefile_custom_cc_flags_spooles_arpack.patch32
-rw-r--r--sci-libs/calculix-cgx/Manifest4
-rw-r--r--sci-libs/calculix-cgx/calculix-cgx-2.10.ebuild (renamed from sci-libs/calculix-cgx/calculix-cgx-2.7-r1.ebuild)31
-rw-r--r--sci-libs/calculix-cgx/files/01_cgx_2.10_Makefile_custom_cxx_flags.patch (renamed from sci-libs/calculix-cgx/files/01_cgx_2.7_Makefile_custom_cxx_flags.patch)33
-rw-r--r--sci-libs/calculix-cgx/files/02_cgx_2.10_menu_fix-freeglut_2.8.1.patch (renamed from sci-libs/calculix-cgx/files/02_cgx_2.7_menu_fix-freeglut_2.8.1.patch)35
-rw-r--r--sci-libs/clfft/Manifest1
-rw-r--r--sci-libs/clfft/clfft-2.10.2.ebuild53
-rw-r--r--sci-libs/io_lib/Manifest1
-rw-r--r--sci-libs/io_lib/io_lib-1.14.7.ebuild29
-rw-r--r--sci-libs/io_lib/metadata.xml17
-rw-r--r--sys-cluster/modules/modules-3.2.10-r1.ebuild2
121 files changed, 2167 insertions, 730 deletions
diff --git a/.travis.yml b/.travis.yml
index d5b6eb4b3..b19309fa9 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,7 +6,7 @@ language: python
python:
- pypy
env:
- - PORTAGE_VER="2.2.27"
+ - PORTAGE_VER="2.2.28"
before_install:
- sudo apt-get -qq update
- sudo apt-get install -y libxml2
@@ -31,12 +31,12 @@ before_script:
- SIZE=$(stat -c %s .travis.yml.upstream)
- if ! cmp -n $SIZE -s .travis.yml .travis.yml.upstream; then echo -e "\e[31m !!! .travis.yml outdated! Update available https://github.com/mrueg/repoman-travis \e[0m" > /tmp/update ; fi
- cd travis-overlay
+ - wget "https://raw.githubusercontent.com/mgorny/gentoo-xml-schema/master/metadata.xsd" -O metadata.xsd
script:
- ./../spinner.sh "python ../portage-${PORTAGE_VER}/bin/repoman full -d"
# You can append own scripts after this line
-
- - wget "https://raw.githubusercontent.com/mgorny/gentoo-xml-schema/master/metadata.xsd" -O metadata.xsd
- - xmllint --noout --schema metadata.xsd */*/metadata.xml 2>&1 | grep "fails to validate"; [[ ${PIPESTATUS[0]} == 0 ]] || exit 1
+ #too old xmllint on travis
+ #- xmllint --noout --schema metadata.xsd */*/metadata.xml 2>&1 | grep "fails to validate"; [[ ${PIPESTATUS[0]} == 0 ]] || false
notifications:
irc: "chat.freenode.net#gentoo-science"
diff --git a/dev-python/hdf5storage/Manifest b/dev-python/hdf5storage/Manifest
index 5b5f79bad..a597e1f14 100644
--- a/dev-python/hdf5storage/Manifest
+++ b/dev-python/hdf5storage/Manifest
@@ -1 +1,2 @@
DIST hdf5storage-0.1.11.zip 112352 SHA256 1eb56cba56a057b4bb27e8547789376d130c1c589f5677d0a7b576524ff0de49 SHA512 c0d57223d7480c72685e158140b0f60b4832bbcc18cfecd7ea1dc5f1a59ae82286d5dedcccbac5834d7f455749df6be9ba9c6bcf58e69ecb874be5a84b87221b WHIRLPOOL de193d20784263d886be9452e55534fb4d98336b00b64df73610eb9be46a85129dd144f3431418406629656d81a0f402b17bafca4b0c25a62a21e846b0cb6e44
+DIST hdf5storage-0.1.13.zip 115134 SHA256 e3d88297f7100812ab8d92e0bb718f6b0e8ef1d3cc202f2dd00f467834d362f8 SHA512 d6c4259e3f387bf58fbd1d4db739a3172b5c3c716b6930e4b65d431d852a93299c4e2e3075c1714ec184106d559f8e4e560b36338eb5ced1adb454e377a079df WHIRLPOOL 1a5aba3e7c6d087bd69954806ef754f7d8f13d258c7fc674cbbbca67f260cf9d20ea9448b42acabd7bc78d7a44df1c2c9ff7ab899b97f6cef242e87d86d2aa8e
diff --git a/dev-python/hdf5storage/hdf5storage-0.1.13.ebuild b/dev-python/hdf5storage/hdf5storage-0.1.13.ebuild
new file mode 100644
index 000000000..9efada42e
--- /dev/null
+++ b/dev-python/hdf5storage/hdf5storage-0.1.13.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+PYTHON_COMPAT=( python2_7 python3_{3,4,5} )
+
+inherit distutils-r1
+
+DESCRIPTION="Read/write Python types to/from HDF5 files, including MATLAB v7.3 MAT files"
+HOMEPAGE="https://github.com/frejanordsiek/hdf5storage"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.zip"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+ "
+DEPEND="${RDEPEND}" \ No newline at end of file
diff --git a/dev-python/matplotlib2tikz/Manifest b/dev-python/matplotlib2tikz/Manifest
index 42208953d..a0e32a355 100644
--- a/dev-python/matplotlib2tikz/Manifest
+++ b/dev-python/matplotlib2tikz/Manifest
@@ -1 +1,2 @@
DIST matplotlib2tikz-0.5.4.tar.gz 22767 SHA256 c4d1e475431a956c0374e12151d14b202861ae3c2beff14c0c56d139151332f9 SHA512 bad02eaa89d3fa3252da9c785df4c991a6a35c3056f0446bba936e8787012bd2269f6ef1b65d4583f1d832b185dd3103491ed6ef28a5ecd9ef99bfa001a60cda WHIRLPOOL eb18e6b09632606930858c1dac7b7658ed41c4efb538515e932ab74e320e03cf5efc34c0ff370a0cd58576e3bd3acfda3908dc64194b392e7160f6c188dc227f
+DIST matplotlib2tikz-0.5.6.tar.gz 22808 SHA256 45e704e112d93bdbea14ed14f350d52ad954fb0cef393b83fa03d1ffbc428d96 SHA512 989543a19cab3ff1957d7eadcc5c192fa6903445aead2dd090a81ceac6832267b859896c27504311bf05de8d92b0bb304d2bcdab8612b7b007b2b9b59febdfe2 WHIRLPOOL ddb682a572897d88e443ff6657a17403a4a25c6fc63fed9d67afa9f483e2e9f4717a29bb843bf042626d763c48e257fea895e0f39dbad5a4801011edb052e5bc
diff --git a/dev-python/matplotlib2tikz/matplotlib2tikz-0.5.6.ebuild b/dev-python/matplotlib2tikz/matplotlib2tikz-0.5.6.ebuild
new file mode 100644
index 000000000..ec78e4f0b
--- /dev/null
+++ b/dev-python/matplotlib2tikz/matplotlib2tikz-0.5.6.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{3,4,5} )
+
+inherit distutils-r1
+
+DESCRIPTION="Convert matplotlib figures into native Pgfplots (TikZ) figures"
+HOMEPAGE="https://github.com/nschloe/matplotlib2tikz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+KEYWORDS="~amd64"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+
+RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-texlive/texlive-pictures"
+DEPEND="${RDEPEND}"
+ #test? ( dev-python/pytest[${PYTHON_USEDEP}] )"
diff --git a/sci-biology/CONTIGuator/CONTIGuator-2.7.3.ebuild b/sci-biology/CONTIGuator/CONTIGuator-2.7.3.ebuild
new file mode 100644
index 000000000..b86613b8b
--- /dev/null
+++ b/sci-biology/CONTIGuator/CONTIGuator-2.7.3.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+DESCRIPTION="Speed up bacterial genome assemblies by artemis and compare chromosome regions"
+HOMEPAGE="http://contiguator.sourceforge.net"
+SRC_URI="http://downloads.sourceforge.net/project/contiguator/CONTIGuator_v2.7.tar.gz
+ https://sourceforge.net/projects/contiguator/files/README.md"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ >=sci-biology/abacas-1.3.1
+ sci-biology/primer3
+ || ( sci-biology/ncbi-tools++ sci-biology/ncbi-blast+ )
+ sci-biology/biopython
+ sci-biology/mummer
+ || ( sci-biology/artemis || ( sci-biology/artemis-bin sci-biology/act-bin ) )"
+
+S="${WORKDIR}"/CONTIGuator_v"${PV}"
+
+src_install(){
+ dobin CONTIGuator.py
+ dodoc Manual.pdf "${DISTDIR}"/README.md
+}
diff --git a/sci-biology/CONTIGuator/CONTIGuator-2.7.ebuild b/sci-biology/CONTIGuator/CONTIGuator-2.7.ebuild
deleted file mode 100644
index 6609fc062..000000000
--- a/sci-biology/CONTIGuator/CONTIGuator-2.7.ebuild
+++ /dev/null
@@ -1,17 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-DESCRIPTION="Speed up bacterial genome assemblies by artemis and compare chromosome regions"
-HOMEPAGE="http://contiguator.sourceforge.net"
-SRC_URI="http://downloads.sourceforge.net/project/contiguator/CONTIGuator_v2.7.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="( sci-biology/artemis sci-biology/artemis-bin )"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/CONTIGuator/Manifest b/sci-biology/CONTIGuator/Manifest
index a0dba3efa..480e6cc23 100644
--- a/sci-biology/CONTIGuator/Manifest
+++ b/sci-biology/CONTIGuator/Manifest
@@ -1 +1,2 @@
DIST CONTIGuator_v2.7.tar.gz 2348570 SHA256 f220dedc85185c168d3164361571225393b7176368237ad2eaa29222a5287da2 SHA512 a958ea6b8a80132460d66075659d637d662f57573a92bca772491e7a5b9fe2436e77b844c0a8e2309646b87771fe56f2a1262c3a6d2054a947fd239166e81718 WHIRLPOOL 8ab9493207297609bd707b1d70e2784675d5c120a4ae4b4e2d883af2e01636e021042601e3f13b5f30b964e5284dcef8e284a5af1129884439bd21208e9b257e
+DIST README.md 8033 SHA256 eaad938a549ac645ce923e80d9244fc9e2f6490c7de96befad3e8fd877cfa215 SHA512 3f57c28c19c3ce67e30feb82a2e616a44aab6a6b70d418f81e335c9e1a862ec501c844bc7c2065ce2c1c6f1e2c44d93f647c96896ccf473c8916cc1d786e6420 WHIRLPOOL 3501466eaf0fb85115cb607e62b19cc634feee2d85ed27af8f709843f9c3e64cbce71cfccafcb24b1ef70dcb5c7f40a683bad8cfb03f490031aeb805bdd91b8e
diff --git a/sci-biology/DisEMBL/DisEMBL-1.4.ebuild b/sci-biology/DisEMBL/DisEMBL-1.4.ebuild
index 4007bdc31..524b3e6c3 100644
--- a/sci-biology/DisEMBL/DisEMBL-1.4.ebuild
+++ b/sci-biology/DisEMBL/DisEMBL-1.4.ebuild
@@ -18,7 +18,7 @@ IUSE=""
# The smoothing function sav_gol.c cannot be re-distributed but can be downloaded from TISEAN.
# http://www.mpipks-dresden.mpg.de/~tisean/
-DEPEND=""
+DEPEND="sci-mathematics/tisean"
RDEPEND="${DEPEND}
sci-biology/biopython"
diff --git a/sci-biology/MolBioLib/Manifest b/sci-biology/MolBioLib/Manifest
new file mode 100644
index 000000000..63714ecca
--- /dev/null
+++ b/sci-biology/MolBioLib/Manifest
@@ -0,0 +1 @@
+DIST MolBioLib_public.version5.tar.gz 2414384 SHA256 694a5682a09caea46dc531bb48a68817873633a31aa92177eb2ba0a253a38eb9 SHA512 056c38bcb65b845b32678fb8c5d758023154c07085414194e98e58281e61e475dca7321c8d684955c88bf459bc92c9d39f8b6091d0b804581e6f6e6ecabe3832 WHIRLPOOL 6d089274ed3f505eb887536b5a4d46e5bbb82951c27fbf684fb820605a6fb416a7e888c9d1a613cb29a3cf5a2b43a192a0781f56a769b793a8986097d2411e43
diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild b/sci-biology/MolBioLib/MolBioLib-5.ebuild
new file mode 100644
index 000000000..5cb9ea210
--- /dev/null
+++ b/sci-biology/MolBioLib/MolBioLib-5.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+DESCRIPTION="C++11 framework for rapid develop and deploy of bioinformatic tasks"
+HOMEPAGE="https://sourceforge.net/projects/molbiolib"
+SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.version${PV}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62) which contains jsoncpp
+# also needs app-doc/doxygen
+DEPEND="dev-lang/perl
+ sys-devel/gcc:*
+ sys-devel/clang
+ >=sci-biology/samtools-0.1.18:0
+ <sci-biology/samtools-1:0"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/MolBioLib
+
+src_compile(){
+ perl MakeAllApps.pl || die
+}
+
+# src_install() needs to be written
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/MolBioLib/metadata.xml
index 959160fe4..f68a1b6fa 100644
--- a/sci-biology/abyss/metadata.xml
+++ b/sci-biology/MolBioLib/metadata.xml
@@ -1,6 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
<maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
diff --git a/sci-biology/ONTO-PERL/ONTO-PERL-1.41.ebuild b/sci-biology/ONTO-PERL/ONTO-PERL-1.41.ebuild
index bb6c9cfda..d6467ee8b 100644
--- a/sci-biology/ONTO-PERL/ONTO-PERL-1.41.ebuild
+++ b/sci-biology/ONTO-PERL/ONTO-PERL-1.41.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
MODULE_AUTHOR=EASR
@@ -17,7 +17,7 @@ IUSE=""
RDEPEND="
>=sci-biology/swissknife-1.65
- dev-perl/DateManip
+ dev-perl/Date-Manip
>=dev-perl/XML-Simple-2.16
>=dev-perl/XML-Parser-2.34
virtual/perl-File-Path"
diff --git a/sci-biology/TransDecoder/Manifest b/sci-biology/TransDecoder/Manifest
index 83f501c15..01bcf6532 100644
--- a/sci-biology/TransDecoder/Manifest
+++ b/sci-biology/TransDecoder/Manifest
@@ -1 +1,2 @@
DIST TransDecoder-2.0.1.tar.gz 9925281 SHA256 ce069da72c8a04e739f8c057af4f97187bf587d3f0d3db40465dfc2c89393e22 SHA512 fd12aeda089a12036e288e58eb0a3c3b9bb1f104f6821102d84ba6ddaec1a9dd32ec7937cd87129ff9814c7c8e26b6b98d27c6af8edd7ed6b5335c4878f649de WHIRLPOOL 61c6b7fe5684becdb28a3bccb113fea07889a2c4e6627e92cd27c1a90ca53f5a88504e048363a1322f1108dd6ebd5549c52aee9d438fbcfb2023390c79c126ec
+DIST TransDecoder-2.1.0.tar.gz 11500688 SHA256 681a8dd72e482cb322d74d8431ddcda61f25c53ad5453d0e22c02c92b2157b24 SHA512 4635a544ef56718db3fbfbe84ab47dfd7af605df73ead69c98e79dca64649c91d6d5139f0b5540d307f23fce5d0d75289c4fd1bedffc393721ccd9b863b7b043 WHIRLPOOL 9c8200e77c5c25384c87bdfe6daeac51336c61abcf6cc247f01f1b80aa0c9eb1a6c70f008ca3b09522fef3988583c520d1634d18bfcabe81eccad772fb7e433e
diff --git a/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
new file mode 100644
index 000000000..9fbcea5ca
--- /dev/null
+++ b/sci-biology/TransDecoder/TransDecoder-2.1.0.ebuild
@@ -0,0 +1,83 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+[ "$PV" == "9999" ] && inherit git-r3
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
+DESCRIPTION="Extract ORF/CDS regions from FASTA sequences"
+HOMEPAGE="http://transdecoder.github.io"
+if [ "$PV" == "9999" ]; then
+ EGIT_REPO_URI="https://github.com/TransDecoder/TransDecoder.git"
+ KEYWORDS=""
+else
+ SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/v"${PV}".tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64"
+ S="${WORKDIR}"/TransDecoder-"${PV}"
+fi
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/cd-hit
+ sci-biology/parafly
+ sci-biology/ffindex"
+
+src_prepare(){
+ rm -rf transdecoder_plugins/cd-hit
+ for f in PerlLib/*.pm; do
+ p=`basename $f .pm`;
+ sed -e "s#use $p;#use TransDecoder::$p;#" -i PerlLib/*.pm util/*.pl TransDecoder.LongOrfs TransDecoder.Predict || die;
+ done
+ epatch "${FILESDIR}"/"${P}"__fix_paths.patch
+ epatch "${FILESDIR}"/pfam_runner.pl.patch
+}
+
+src_compile(){
+ einfo "Skipping compilation of bundled cd-hit code, nothing else to do"
+}
+
+# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see
+# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704"
+# thread in archives. You can get it from
+# http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin
+
+src_install(){
+ dobin TransDecoder.Predict TransDecoder.LongOrfs
+ insinto /usr/share/${PN}/util
+ doins util/*.pl
+ chmod -R a+rx "${D}"/usr/share/${PN}/util
+ # zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin
+ rm -rf util/bin
+ #
+ # * sci-biology/trinityrnaseq-20140413:0::science
+ # * /usr/bin/Fasta_reader.pm
+ # * /usr/bin/GFF3_utils.pm
+ # * /usr/bin/Gene_obj.pm
+ # * /usr/bin/Gene_obj_indexer.pm
+ # * /usr/bin/Longest_orf.pm
+ # * /usr/bin/Nuc_translator.pm
+ # * /usr/bin/TiedHash.pm
+ #
+ perl_set_version
+ insinto ${VENDOR_LIB}/${PN}
+ doins PerlLib/*.pm
+ # dodoc Release.Notes
+ einfo "Fetch your own Pfam-A.hmm (Pfam-AB.hmm is discontinued since 05/2015):"
+ einfo "wget --mirror -nH -nd ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz"
+ einfo "hmmpress Pfam-A.hmm.bin"
+}
+
+pkg_postinst(){
+ einfo "It is recommended to use TransDecoder with sci-biology/hmmer-3 or"
+ einfo "at least with NCBI blast from either:"
+ einfo " sci-biology/ncbi-blast+ (released more often) or from"
+ einfo " sci-biology/ncbi-toolkit++ (a huge bundle with releases and less frequent bugfixes)"
+}
diff --git a/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch b/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch
new file mode 100644
index 000000000..0a6fca050
--- /dev/null
+++ b/sci-biology/TransDecoder/files/TransDecoder-2.1.0__fix_paths.patch
@@ -0,0 +1,22 @@
+--- TransDecoder-2.0.1/TransDecoder.LongOrfs.ori 2015-11-19 21:05:53.340219051 +0100
++++ TransDecoder-2.0.1/TransDecoder.LongOrfs 2015-11-19 21:20:44.870221380 +0100
+@@ -64,7 +64,7 @@
+ use TransDecoder::Fasta_reader;
+ use TransDecoder::Longest_orf;
+
+-my $UTIL_DIR = "$FindBin::RealBin/util";
++my $UTIL_DIR = "/usr/share/TransDecoder/util/";
+ $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
+
+
+--- TransDecoder-2.0.1/TransDecoder.Predict.ori 2015-11-19 21:06:04.280219080 +0100
++++ TransDecoder-2.0.1/TransDecoder.Predict 2015-11-19 21:21:22.560221479 +0100
+@@ -52,7 +52,7 @@
+ use TransDecoder::Fasta_reader;
+ use TransDecoder::Longest_orf;
+
+-my $UTIL_DIR = "$FindBin::RealBin/util";
++my $UTIL_DIR = "/usr/share/TransDecoder/util/";
+ $ENV{PATH} = "$UTIL_DIR/bin:$ENV{PATH}";
+
+
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
deleted file mode 100644
index 77dfde1ec..000000000
--- a/sci-biology/abyss/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST abyss-1.3.3.tar.gz 621480 SHA256 60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512 4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2 WHIRLPOOL 35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914
-DIST abyss-1.3.4.tar.gz 640545 SHA256 6b6ccb04baaa9d244dd67d95e1512a934d2e54fd28a539149b6845ed5c496baf SHA512 0fa4c14117699945e007412deaeeccca27124a210669accbc1444baf5a4de1a17e1f9b48e6ee43fefed63f0d56b933c847363e59a0fc2bad60ae6d603cd8c09e WHIRLPOOL 42b16f22bc47c8f29b07c256d504d6f58119c64fdcf0e198fd8b836ceb45139fd5cadc7feec72adf958800e55eb1065a449ce7dd288339887dcea4ab13623c01
-DIST abyss-1.3.6.tar.gz 678880 SHA256 4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512 2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace WHIRLPOOL 0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07
diff --git a/sci-biology/abyss/abyss-1.3.3-r1.ebuild b/sci-biology/abyss/abyss-1.3.3-r1.ebuild
deleted file mode 100644
index 76f15b496..000000000
--- a/sci-biology/abyss/abyss-1.3.3-r1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit autotools eutils toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- dev-cpp/sparsehash
- mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-src_prepare() {
- tc-export AR
- epatch \
- "${FILESDIR}"/${P}-gcc-4.7.patch \
- "${FILESDIR}"/${P}-ac_prog_ar.patch \
- "${FILESDIR}"/${P}-samtoafg.patch
-
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- eautoreconf
-}
-
-src_configure() {
- econf \
- --docdir="${EPREFIX}/usr/share/doc/${PF}" \
- $(use_enable openmp)
-}
diff --git a/sci-biology/abyss/abyss-1.3.4-r1.ebuild b/sci-biology/abyss/abyss-1.3.4-r1.ebuild
deleted file mode 100644
index 762d49a79..000000000
--- a/sci-biology/abyss/abyss-1.3.4-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- dev-cpp/sparsehash
- mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-PATCHES=(
- "${FILESDIR}"/${P}-gcc-4.7.patch
- "${FILESDIR}"/${PN}-1.3.3-ac_prog_ar.patch
- "${FILESDIR}"/${P}-samtoafg.patch
- )
-
-src_prepare() {
- tc-export AR
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- autotools-utils_src_prepare
-}
-
-src_configure() {
- local myeconfargs=(
- --docdir="${EPREFIX}/usr/share/doc/${PF}"
- $(use_enable openmp)
- )
- autotools-utils_src_configure
-}
diff --git a/sci-biology/abyss/abyss-1.3.6-r1.ebuild b/sci-biology/abyss/abyss-1.3.6-r1.ebuild
deleted file mode 100644
index f002a9578..000000000
--- a/sci-biology/abyss/abyss-1.3.6-r1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- dev-cpp/sparsehash
- dev-libs/boost
- mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-PATCHES=(
- "${FILESDIR}"/${P}-gcc-4.7.patch
- "${FILESDIR}"/${P}-ac_prog_ar.patch
- "${FILESDIR}"/${P}-samtoafg.patch
- )
-
-src_prepare() {
- tc-export AR
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- autotools-utils_src_prepare
-}
-
-src_configure() {
- local myeconfargs=(
- --docdir="${EPREFIX}/usr/share/doc/${PF}"
- $(use_enable openmp)
- )
- autotools-utils_src_configure
-}
diff --git a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch
deleted file mode 100644
index 300868f52..000000000
--- a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch
+++ /dev/null
@@ -1,18 +0,0 @@
- configure.ac | 4 ++++
- 1 file changed, 4 insertions(+)
-
-diff --git a/configure.ac b/configure.ac
-index 5c6cb92..b99bedd 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -12,6 +12,10 @@ AC_PROG_CPP
- AC_PROG_CXX
- AC_PROG_INSTALL
- AC_PROG_RANLIB
-+AN_MAKEVAR([AR], [AC_PROG_AR])
-+AN_PROGRAM([ar], [AC_PROG_AR])
-+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
-+AC_PROG_AR
-
- # Checks for header files.
- AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \
diff --git a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
deleted file mode 100644
index 42066f7f2..000000000
--- a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- ParseAligns/abyss-fixmate.cc | 1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
-index 506ea0c..a0a403c 100644
---- a/ParseAligns/abyss-fixmate.cc
-+++ b/ParseAligns/abyss-fixmate.cc
-@@ -15,6 +15,7 @@
- #include <iterator>
- #include <sstream>
- #include <string>
-+#include <unistd.h>
-
- using namespace std;
-
diff --git a/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch
deleted file mode 100644
index cb7dfb08a..000000000
--- a/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-Hello,
-
-I see Shaun Jackmans' (abyss-)sam2afg script is available within the
-Amos source repository. I find this very useful for coercing output from
-assemblers which which don't track read location into amos by remapping
-reads against the assembly and converting to afg - not ideal but better
-than nothing when you don't have the 'real' read locations to work with.
-
-This fails, however when reads are aligned with 'bwa mem', which can
-output multi-part alignments. sam2afg checks for reuse of the same read
-id (presumably to prevent the generation of non-unique eid values),
-consequently encountering multiple alignments for a read causes it to die.
-
-The following one-line patch allows sam2afg to skip these secondary
-alignments present in 'bwa mem' output, provided bwa mem has been run
-with the '-M' argument which sets the SAM 'secondary alignment' flag on
-the alignments in question.
-
-Hopefully this will also be of use to others...
-
-Best Regards,
-James
-
---
-Dr. James Abbott
-Lead Bioinformatician
-Bioinformatics Support Service
-Imperial College, London
-
-
---- abyss-1.3.6/bin/abyss-samtoafg.ori 2015-05-23 23:43:46.797747928 +0200
-+++ abyss-1.3.6/bin/abyss-samtoafg 2015-05-23 23:44:09.227747743 +0200
-@@ -105,6 +105,7 @@
- die unless defined $qqual;
-
- $tstart--; # convert to zero-based coordinate
-+ next if $flag & 0x100; # secondary alignment
- $qid .= "/1" if $flag & 0x40; #FREAD1
- $qid .= "/2" if $flag & 0x80; #FREAD2
-
diff --git a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch
deleted file mode 100644
index c2cc35c31..000000000
--- a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- ParseAligns/abyss-fixmate.cc | 1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
-index 1a169cf..36cc05b 100644
---- a/ParseAligns/abyss-fixmate.cc
-+++ b/ParseAligns/abyss-fixmate.cc
-@@ -16,6 +16,7 @@
- #include <iterator>
- #include <sstream>
- #include <string>
-+#include <unistd.h>
-
- using namespace std;
-
diff --git a/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch
deleted file mode 100644
index cb7dfb08a..000000000
--- a/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-Hello,
-
-I see Shaun Jackmans' (abyss-)sam2afg script is available within the
-Amos source repository. I find this very useful for coercing output from
-assemblers which which don't track read location into amos by remapping
-reads against the assembly and converting to afg - not ideal but better
-than nothing when you don't have the 'real' read locations to work with.
-
-This fails, however when reads are aligned with 'bwa mem', which can
-output multi-part alignments. sam2afg checks for reuse of the same read
-id (presumably to prevent the generation of non-unique eid values),
-consequently encountering multiple alignments for a read causes it to die.
-
-The following one-line patch allows sam2afg to skip these secondary
-alignments present in 'bwa mem' output, provided bwa mem has been run
-with the '-M' argument which sets the SAM 'secondary alignment' flag on
-the alignments in question.
-
-Hopefully this will also be of use to others...
-
-Best Regards,
-James
-
---
-Dr. James Abbott
-Lead Bioinformatician
-Bioinformatics Support Service
-Imperial College, London
-
-
---- abyss-1.3.6/bin/abyss-samtoafg.ori 2015-05-23 23:43:46.797747928 +0200
-+++ abyss-1.3.6/bin/abyss-samtoafg 2015-05-23 23:44:09.227747743 +0200
-@@ -105,6 +105,7 @@
- die unless defined $qqual;
-
- $tstart--; # convert to zero-based coordinate
-+ next if $flag & 0x100; # secondary alignment
- $qid .= "/1" if $flag & 0x40; #FREAD1
- $qid .= "/2" if $flag & 0x80; #FREAD2
-
diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
deleted file mode 100644
index 158e9b126..000000000
--- a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
+++ /dev/null
@@ -1,18 +0,0 @@
- configure.ac | 4 ++++
- 1 file changed, 4 insertions(+)
-
-diff --git a/configure.ac b/configure.ac
-index 9d4bb66..aa94364 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -12,6 +12,10 @@ AC_PROG_CPP
- AC_PROG_CXX
- AC_PROG_INSTALL
- AC_PROG_RANLIB
-+AN_MAKEVAR([AR], [AC_PROG_AR])
-+AN_PROGRAM([ar], [AC_PROG_AR])
-+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
-+AC_PROG_AR
- AC_CHECK_TOOL(GHC, ghc)
- AM_CONDITIONAL([HAVE_GHC], [test "$GHC"])
-
diff --git a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch
deleted file mode 100644
index c2cc35c31..000000000
--- a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- ParseAligns/abyss-fixmate.cc | 1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
-index 1a169cf..36cc05b 100644
---- a/ParseAligns/abyss-fixmate.cc
-+++ b/ParseAligns/abyss-fixmate.cc
-@@ -16,6 +16,7 @@
- #include <iterator>
- #include <sstream>
- #include <string>
-+#include <unistd.h>
-
- using namespace std;
-
diff --git a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch
deleted file mode 100644
index cb7dfb08a..000000000
--- a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-Hello,
-
-I see Shaun Jackmans' (abyss-)sam2afg script is available within the
-Amos source repository. I find this very useful for coercing output from
-assemblers which which don't track read location into amos by remapping
-reads against the assembly and converting to afg - not ideal but better
-than nothing when you don't have the 'real' read locations to work with.
-
-This fails, however when reads are aligned with 'bwa mem', which can
-output multi-part alignments. sam2afg checks for reuse of the same read
-id (presumably to prevent the generation of non-unique eid values),
-consequently encountering multiple alignments for a read causes it to die.
-
-The following one-line patch allows sam2afg to skip these secondary
-alignments present in 'bwa mem' output, provided bwa mem has been run
-with the '-M' argument which sets the SAM 'secondary alignment' flag on
-the alignments in question.
-
-Hopefully this will also be of use to others...
-
-Best Regards,
-James
-
---
-Dr. James Abbott
-Lead Bioinformatician
-Bioinformatics Support Service
-Imperial College, London
-
-
---- abyss-1.3.6/bin/abyss-samtoafg.ori 2015-05-23 23:43:46.797747928 +0200
-+++ abyss-1.3.6/bin/abyss-samtoafg 2015-05-23 23:44:09.227747743 +0200
-@@ -105,6 +105,7 @@
- die unless defined $qqual;
-
- $tstart--; # convert to zero-based coordinate
-+ next if $flag & 0x100; # secondary alignment
- $qid .= "/1" if $flag & 0x40; #FREAD1
- $qid .= "/2" if $flag & 0x80; #FREAD2
-
diff --git a/sci-biology/act-bin/Manifest b/sci-biology/act-bin/Manifest
new file mode 100644
index 000000000..0ca1980c8
--- /dev/null
+++ b/sci-biology/act-bin/Manifest
@@ -0,0 +1,4 @@
+DIST act-bin-13.0.0.html_build.zip 2067725 SHA256 6a07ff70aef13e633884491c83832c150532eb0f199c0c382bab8dd4d23c3f4d SHA512 c119b12a68e52249f3a417c503129b8e538baae218cda07cd4d52b34eab9be7cdbfc86180c6675f26afe8bac556e18b66a94407f00a133c58a2e1c626f6d3571 WHIRLPOOL ca4b5367aabf22e56d394d18d0546d132400fb6d28a9433b9524f89ef181acc06406b7230563444b5a2df8dd08ea4ee740c9b94d928c6830d3e5736723071c41
+DIST act-bin-13.0.0.manual.pdf 946922 SHA256 460adb7a9c5cd6f6e5b0bf499ddec48fddf0c475824c363db9ae8e6e7b1f0ade SHA512 6af8bf6fb9cf762c078288a09cae053c9c08f5d44dd8d7324acaaa73b63d79e107a403c5dbef48a319408e0158d3ace146f6ed29d55cb553e668be711ae73914 WHIRLPOOL 01cbd2cc1139d732f61ea21782dc13935369746c1eee3b83babf07fc47f76425c00297af6c253fddbb9c4d3d16ff3ce9a03a7596dde1419f4128e30b128ec176
+DIST act_v13.jar 11005084 SHA256 5aa943b851a596d7ef9354c495d7fd7b86e05a942bab6f5db4a459fa7a580a19 SHA512 693e55d2c1f71e99f981114aa9715dac7386bedaf6bd753b49ea58f1a4ef30b5f603384cf7c5b43d3c95eebc71dc66eba04e51b0303a80566c0a8d186f473d4d WHIRLPOOL dbbaea5b3c239ceb342ad8b6cf41bdbf995abb58c5cbf28ee4330271ebcd7dc05a336f3154f88e7b0fc3b7aeab5e4a8229eb7628dfa04245b9883e08903ea1ec
+DIST sact_v13.jar 11533674 SHA256 c20b4bc0cafbd4d7aa577009c4ea89a78405230ab44b20aac01c715b03ecd8f6 SHA512 365c82933ebd4c20448a6872c4b3a5ddee313aa137bc83bf8b95a677fa7bcf32920be185971c00116d6e524357975ef633fe25496d124b6001eecdc698afcfaf WHIRLPOOL 22e576045369e251aa93a2da9081c841eaf11cc2f7804a354651ff9f40d4d36d3fed3662bd7596d3b5c633dab0ef688cecaae1bedd049d2dc97fd43f776eaeb0
diff --git a/sci-biology/act-bin/act-bin-13.0.0.ebuild b/sci-biology/act-bin/act-bin-13.0.0.ebuild
new file mode 100644
index 000000000..debf770c0
--- /dev/null
+++ b/sci-biology/act-bin/act-bin-13.0.0.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit java-pkg-2
+
+DESCRIPTION="DNA contig sequence comparison tool supplementing Artemis"
+HOMEPAGE="http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/sact_v13.jar
+ ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_v13.jar
+ ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_manual_complete.pdf -> ${P}.manual.pdf
+ ftp://ftp.sanger.ac.uk/pub/resources/software/act/v13/act_html_build.zip -> ${P}.html_build.zip"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="
+ !sci-biology/artemis"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.6:*"
+
+S="${WORKDIR}"
+
+src_unpack(){
+ unzip "${DISTDIR}"/${P}.html_build.zip || die
+}
+
+src_prepare(){
+ default
+ cd act_html_build || die
+ rm -f .DS_Store HTML.index HTML.manifest || die
+}
+
+src_install(){
+ java-pkg_dojar "${DISTDIR}"/*.jar
+ dodoc "${DISTDIR}"/${P}.manual.pdf
+ insinto /usr/share/doc/"${PN}"/html
+ doins act_html_build/*
+}
+
+pkg_postinst(){
+ einfo "For BAM file support please install sci-biology/BamView"
+ einfo "You may find interesting the additional web resources:"
+ einfo "http://www.webact.org/WebACT"
+ einfo "http://www.hpa-bioinfotools.org.uk/pise/double_act.html"
+}
diff --git a/sci-biology/act-bin/metadata.xml b/sci-biology/act-bin/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/act-bin/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild
index bbf768f08..ff04169bc 100644
--- a/sci-biology/amos/amos-3.1.0-r2.ebuild
+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild
@@ -10,7 +10,7 @@ inherit eutils python-r1
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs
-DESCRIPTION="A Modular, Open-Source whole genome assembler"
+DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies"
HOMEPAGE="http://amos.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
@@ -38,6 +38,9 @@ src_prepare() {
epatch \
"${FILESDIR}"/${P}-gcc-4.7.patch \
"${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
+ # $ gap-links
+ # ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
+ # $
}
# --with-jellyfish location of Jellyfish headers
@@ -57,4 +60,8 @@ src_install() {
# zap the mis-placed files ('make install' is at fault)
rm -f "${D}"/usr/lib64/AMOS/*.pm
rm -rf "${D}"/usr/lib64/TIGR
+ echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die
+ mkdir -p "${ED}"/etc || die
+ touch "${ED}"/etc/amos.acf || die
+ doenvd "${S}/99amos"
}
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index 07a140a97..fca8f2e67 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -10,7 +10,7 @@ inherit perl-module eutils toolchain-funcs
AUTOTOOLS_AUTORECONF=true
inherit autotools-utils git-r3
-DESCRIPTION="Genome assembly package live cvs sources"
+DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies"
HOMEPAGE="http://sourceforge.net/projects/amos"
SRC_URI=""
EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos"
@@ -34,6 +34,10 @@ RDEPEND="${DEPEND}
# --with-jellyfish location of Jellyfish headers
+# $ gap-links
+# ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
+# $
+
src_install() {
default
python_replicate_script "${ED}"/usr/bin/goBambus2
@@ -49,4 +53,8 @@ src_install() {
# zap the mis-placed files ('make install' is at fault)
rm -f "${D}"/usr/lib64/AMOS/*.pm
rm -rf "${D}"/usr/lib64/TIGR
+ echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die
+ mkdir -p "${ED}"/etc || die
+ touch "${ED}"/etc/amos.acf || die
+ doenvd "${S}/99amos"
}
diff --git a/sci-biology/arachne/Manifest b/sci-biology/arachne/Manifest
new file mode 100644
index 000000000..c06393105
--- /dev/null
+++ b/sci-biology/arachne/Manifest
@@ -0,0 +1 @@
+DIST arachne-46233.tar.gz 5161566 SHA256 1b2c254a19b4792ec8a6c32ffc3d97c20e43deea3141ee975995221c7ccdf990 SHA512 4ab293e7f4477dd6aeba7c6bc1a78d168cbb811d7f67cbcbc1eea094a7b6bd180bdde6fb1b7c8256ff473dba3d748a43bd426d971575f1c0793289a0b200dc2b WHIRLPOOL 9d18c31fba1e69690d6a20c75b47319298b56c7a73ede0fed55e1d4b30c7783bc7f5d5f54346b1fb05376c54854c4ba7f2f89401bda178c5aac8e39957292ff8
diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild
new file mode 100644
index 000000000..71fc0b87e
--- /dev/null
+++ b/sci-biology/arachne/arachne-46233.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Whole genome shotgun assembler for Sanger read lengths (overlap-layout-contig)"
+HOMEPAGE="https://www.broadinstitute.org/crd/wiki
+ http://genome.cshlp.org/content/12/1/177.abstract"
+SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz"
+
+LICENSE="MIT" # not exactly MIT ... hence no KEYWORDS
+SLOT="0"
+KEYWORDS=""
+IUSE="doc openmp"
+
+DEPEND="dev-libs/xerces-c
+ doc? ( virtual/latex-base app-text/dvipsk )"
+RDEPEND="${DEPEND}"
+
+# needs >=g++-4.7 but does not compile with 5.3.0
+
+# --disable-openmp to disable requirement for OpenMP-capable compiler
+src_configure() {
+ local myconf=()
+ use openmp || myconf+=( --disable-openmp )
+ econf ${myconf[@]}
+}
+
+# set the following environment variables
+# http://www.broadinstitute.org/crd/wiki/index.php/Setup
+#
+# ARACHNE_PRE
+# ARACHNE_BIN_DIR
+# ARACHNE_PRETTY_HELP
+
+pkg_postinst(){
+ einfo "Please add these to your ~/.bashrc"
+ einfo "limit stacksize 100000"
+ einfo "limit datasize unlimited"
+}
diff --git a/sci-biology/arachne/metadata.xml b/sci-biology/arachne/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/arachne/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/artemis-bin/Manifest b/sci-biology/artemis-bin/Manifest
index 3bd261d96..5ea64c9bf 100644
--- a/sci-biology/artemis-bin/Manifest
+++ b/sci-biology/artemis-bin/Manifest
@@ -1,4 +1,6 @@
-DIST artemis.pdf 1149449 SHA256 ab573b4ea7b895cb7d2a97e4d42a71938f1feda44e2da22fe5b079583ad87ba6 SHA512 1c3056dab7239c3a68b2e76491d77612f22ac8f83eaf32e0ab0a3901e03d3c65d5ac02f5758d2d7728d94dd44c29517a498fa94a947d5d319ded43ddec4ba5fb WHIRLPOOL a75266ae72075ea7547560a9046c1e0f813956b94a5c3d9af3cd08a579ed60af842c6ece94e6b1dfa5db1820094069edb7d88b4ee6256410ebced4310739d79f
+DIST artemis-bin-16.0.11.html_build.zip 2284822 SHA256 d78ecbf8906395ca27bb3d45ebeae05a792923c98866632468dd2cd26c9bbddf SHA512 80c952fe20f98b647f38a08a469cb351bb44aa1b0a7d1a9b997fabbd37107d5d934a6d52fa2abfde243f90f4e752c99d418c4ad6b634d82de9744d089eb1cf8a WHIRLPOOL ea67f08ebf8284a186690880d7185e8991e1616f782fbde640021f44085dd6247d065e3bdae557aa10af0b2584a7f40421b9ae6199328f677f17082fa7716759
+DIST artemis-bin-16.0.11.manual.pdf 1149449 SHA256 ab573b4ea7b895cb7d2a97e4d42a71938f1feda44e2da22fe5b079583ad87ba6 SHA512 1c3056dab7239c3a68b2e76491d77612f22ac8f83eaf32e0ab0a3901e03d3c65d5ac02f5758d2d7728d94dd44c29517a498fa94a947d5d319ded43ddec4ba5fb WHIRLPOOL a75266ae72075ea7547560a9046c1e0f813956b94a5c3d9af3cd08a579ed60af842c6ece94e6b1dfa5db1820094069edb7d88b4ee6256410ebced4310739d79f
+DIST artemis-bin-16.0.11.release_notes.txt 2727 SHA256 f1facd291ffbe21758516eec421297ed8d4ddfa0f9d8ba5c201045e0aa56e648 SHA512 a9fadad47ee50a54b4036193afa6fa74e404c6b6cfd61e97885c8824f885d162c4b826910223ce1930ee55b74fe40e365c7d66019746d2fb2d70ecd3c1ceacb6 WHIRLPOOL c9fafe943b6c1e833effff8c004031d6e1156b312878aa099de57ecac6f3e2461f5675a8cf49830db7e0c8b0107516844e9c64d81d6ba8dcaf48faea912dc6d1
DIST artemis_compiled_v16.0.11.tar.gz 10722613 SHA256 0413c3f0deab4d813bc4f3af7aef8cca09ad2111b3497a0696c18a31857ffd4b SHA512 a0fb9f64b0fb869bde9fe2d1788ed938a16ea0bd75315abd93e65af89772fe9d4589b7e7813286c9b1d90f1f3133c16d9bc35ce78d1740c5631ca0e32633e421 WHIRLPOOL 0682bdfead9f95a17180816ed445226c128a804f8db3549c78627b510330694b60fd7ab0e419766bf08295f3a266eefd0dfd85c0d1244c80009b5aba0c29052a
DIST artemis_v16.0.11.jar 11292419 SHA256 f368714105646cfc31460cfcfb72b8b33490c7684ee5323d7dd181060039c80f SHA512 2fbd7c5ab12c2ca710906324eb5ee861d4821eaf923f630a800ce2b2de4e43c3971cf6c470140aa2654741ab79440a2039e8b9a17502ca955432d9ef311e9f84 WHIRLPOOL fc605625b536853ee7657b09bca93f04b9f1da67a093875bcfac0d4948f7daf020c26f0624b551aba36f21e87a7ee8b933e0e26c45a715ea2fe6cb9211d0f78f
DIST sartemis_v16.0.11.jar 11832144 SHA256 834ad0464405843904b173f38220f47867ec8eb779cb2c37d6de7ba585ef133c SHA512 6fd63ac81eed727816fe633cde3e9fab9eaf71a61c74aef4f82c8c4dc24efe93ce86494ebdf3fcb3d82e50aed5c277f383f67c1b7b68ae81cf872f2982bc1850 WHIRLPOOL 874ab57f11b011a222efd4b91278614941b096756faf0259b844453dfb082d99bae503faa2ffaeb6c4d56b4317b3bcc00a49f8b5b16d6c7cc02968b4911c503a
diff --git a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
index e0c9fe997..2949569f4 100644
--- a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
+++ b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
@@ -1,25 +1,27 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
inherit java-pkg-2
MY_V="16"
-DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool"
+DESCRIPTION="DNA sequence viewer, annotation (Artemis) without comparison (ACT) tool"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_compiled_v"${PV}".tar.gz
ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_v"${PV}".jar
ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/sartemis_v"${PV}".jar
- ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf"
+ ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/artemis_manual_complete.pdf -> ${P}.manual.pdf
+ ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/release_notes.txt -> ${P}.release_notes.txt
+ ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/art_html_build.zip -> ${P}.html_build.zip"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-S="${WORKDIR}"/artemis
+S="${WORKDIR}"
DEPEND="
!sci-biology/artemis
@@ -27,12 +29,24 @@ DEPEND="
RDEPEND="${DEPEND}
>=virtual/jre-1.6"
+src_unpack(){
+ unzip "${DISTDIR}"/${P}.html_build.zip || die
+}
+
+src_prepare(){
+ default
+ cd art_html_build || die
+ rm -f .DS_Store HTML.index HTML.manifest || die
+}
+
src_install(){
cp -p "${DISTDIR}"/artemis_v"${PV}".jar artemis.jar || die
java-pkg_dojar artemis.jar
cp -p "${DISTDIR}"/sartemis_v"${PV}".jar sartemis.jar || die
java-pkg_dojar sartemis.jar
- dodoc "${DISTDIR}"/artemis.pdf README
+ dodoc "${DISTDIR}"/${P}.manual.pdf "${DISTDIR}"/${P}.release_notes.txt
+ insinto /usr/share/doc/"${PN}"/html
+ doins art_html_build/*
}
# artemis_compiled_v16.0.11.tar.gz contains compiled binaries but also java *.class files
@@ -41,4 +55,7 @@ src_install(){
pkg_postinst(){
einfo "For BAM file support please install sci-biology/BamView"
+ einfo "You may find interesting the additional web resources:"
+ einfo "http://www.webact.org/WebACT"
+ einfo "http://www.hpa-bioinfotools.org.uk/pise/double_act.html"
}
diff --git a/sci-biology/artemis/Manifest b/sci-biology/artemis/Manifest
index 1c027d782..0a68bacef 100644
--- a/sci-biology/artemis/Manifest
+++ b/sci-biology/artemis/Manifest
@@ -1 +1,2 @@
-DIST artemis.pdf 1149449 SHA256 ab573b4ea7b895cb7d2a97e4d42a71938f1feda44e2da22fe5b079583ad87ba6 SHA512 1c3056dab7239c3a68b2e76491d77612f22ac8f83eaf32e0ab0a3901e03d3c65d5ac02f5758d2d7728d94dd44c29517a498fa94a947d5d319ded43ddec4ba5fb WHIRLPOOL a75266ae72075ea7547560a9046c1e0f813956b94a5c3d9af3cd08a579ed60af842c6ece94e6b1dfa5db1820094069edb7d88b4ee6256410ebced4310739d79f
+DIST artemis-9999.html_build.zip 2284822 SHA256 d78ecbf8906395ca27bb3d45ebeae05a792923c98866632468dd2cd26c9bbddf SHA512 80c952fe20f98b647f38a08a469cb351bb44aa1b0a7d1a9b997fabbd37107d5d934a6d52fa2abfde243f90f4e752c99d418c4ad6b634d82de9744d089eb1cf8a WHIRLPOOL ea67f08ebf8284a186690880d7185e8991e1616f782fbde640021f44085dd6247d065e3bdae557aa10af0b2584a7f40421b9ae6199328f677f17082fa7716759
+DIST artemis-9999.manual.pdf 1149449 SHA256 ab573b4ea7b895cb7d2a97e4d42a71938f1feda44e2da22fe5b079583ad87ba6 SHA512 1c3056dab7239c3a68b2e76491d77612f22ac8f83eaf32e0ab0a3901e03d3c65d5ac02f5758d2d7728d94dd44c29517a498fa94a947d5d319ded43ddec4ba5fb WHIRLPOOL a75266ae72075ea7547560a9046c1e0f813956b94a5c3d9af3cd08a579ed60af842c6ece94e6b1dfa5db1820094069edb7d88b4ee6256410ebced4310739d79f
diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
index 81da9cba2..d9e915dfc 100644
--- a/sci-biology/artemis/artemis-9999.ebuild
+++ b/sci-biology/artemis/artemis-9999.ebuild
@@ -1,14 +1,15 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
inherit java-pkg-2 java-ant-2 git-r3
DESCRIPTION="DNA sequence viewer/annotation (Artemis) and comparison (ACT) tool"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf -> ${P}.manual.pdf
+ ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/art_html_build.zip -> ${P}.html_build.zip"
EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
LICENSE="GPL-2"
@@ -41,6 +42,10 @@ DEPEND="${RDEPEND}
# BamView is at http://bamview.sourceforge.net/
+src_unpack(){
+ unzip "${DISTDIR}"/art_html_build.zip || die
+}
+
src_compile(){
ant || die
}
@@ -48,7 +53,9 @@ src_compile(){
src_install(){
dobin act act.command art dnaplotter gff2embl
java-pkg_dojar ant-build/artemis.jar
- dodoc "${DISTDIR}"/artemis.pdf README
+ dodoc "${DISTDIR}"/"${P}".manual.pdf README
+ insinto /usr/share/doc/"${PN}"/html
+ doins art_html_build/*
}
# artemis_compiled_v16.0.11.tar.gz contains compiled binaries but also java *.class files
@@ -57,5 +64,7 @@ src_install(){
pkg_postinst(){
einfo "For BAM file support please install sci-biology/BamView"
- einfo " from http://bamview.sourceforge.net"
+ einfo "You may find interesting the additional web resources:"
+ einfo "http://www.webact.org/WebACT"
+ einfo "http://www.hpa-bioinfotools.org.uk/pise/double_act.html"
}
diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest
new file mode 100644
index 000000000..67377b14c
--- /dev/null
+++ b/sci-biology/bamtools/Manifest
@@ -0,0 +1 @@
+DIST bamtools-2.4.0.tar.gz 539779 SHA256 f1fe82b8871719e0fb9ed7be73885f5d0815dd5c7277ee33bd8f67ace961e13e SHA512 33332f290e72ed3943c9df6022a44cfcd358ae1c1d41b1b494c7087a66e865529721ee6230212313d482cb66764573e300f362fee9ccbf3c0da18544bf2e9425 WHIRLPOOL 93097730c225f64c923dcf755df1990d3ba150aef29d227b88f25c9d97bc08745640dfffb05f7b789ff1aa4ef40ae982780be1165dac81717ce27b9664cfebf2
diff --git a/sci-biology/bamtools/bamtools-2.4.0.ebuild b/sci-biology/bamtools/bamtools-2.4.0.ebuild
new file mode 100644
index 000000000..b2d7d623f
--- /dev/null
+++ b/sci-biology/bamtools/bamtools-2.4.0.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils
+
+DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
+HOMEPAGE="https://github.com/pezmaster31/bamtools"
+SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="
+ >=dev-libs/jsoncpp-0.5.0-r1
+ <dev-libs/jsoncpp-1
+ sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+PATCHES=( "${FILESDIR}"/${P}-unbundle.patch )
+
+src_install() {
+ cmake-utils_src_install
+ if ! use static-libs; then
+ rm "${ED}"/usr/$(get_libdir)/*.a || die
+ fi
+}
diff --git a/sci-biology/bamtools/files/bamtools-2.4.0-unbundle.patch b/sci-biology/bamtools/files/bamtools-2.4.0-unbundle.patch
new file mode 100644
index 000000000..c07c59d2c
--- /dev/null
+++ b/sci-biology/bamtools/files/bamtools-2.4.0-unbundle.patch
@@ -0,0 +1,23 @@
+--- bamtools-2.3.0/src/api/CMakeLists.txt.ori 2013-08-27 18:00:43.000000000 +0200
++++ bamtools-2.3.0/src/api/CMakeLists.txt 2013-08-27 18:00:47.000000000 +0200
+@@ -54,8 +54,8 @@
+ target_link_libraries( BamTools-static ${APILibs} )
+
+ # set library install destinations
+-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
+-install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
++install( TARGETS BamTools LIBRARY DESTINATION "lib${LIB_SUFFIX}" RUNTIME DESTINATION "bin")
++install( TARGETS BamTools-static ARCHIVE DESTINATION "lib${LIB_SUFFIX}")
+
+ # export API headers
+ include(../ExportHeader.cmake)
+--- bamtools-2.3.0/src/CMakeLists.txt.ori 2013-08-27 18:03:10.000000000 +0200
++++ bamtools-2.3.0/src/CMakeLists.txt 2013-08-27 18:03:23.000000000 +0200
+@@ -6,7 +6,6 @@
+ # ==========================
+
+ add_subdirectory( api )
+-add_subdirectory( third_party )
+ add_subdirectory( toolkit )
+ add_subdirectory( utils )
+
diff --git a/sci-biology/cap3-bin/Manifest b/sci-biology/cap3-bin/Manifest
index 2b535c029..940c7aed2 100644
--- a/sci-biology/cap3-bin/Manifest
+++ b/sci-biology/cap3-bin/Manifest
@@ -1,2 +1,3 @@
DIST cap3.linux.i686_xeon64.tar 430080 SHA256 fd7112a89dd349e0d11820d4bfab34c3556eb570828f71a8db18b68bd6aa1c2c SHA512 3f0f2434a5fcecf50a5ba0b5fe0400c9c6f1f0eeef860d1a7c84ba6ae266d44679a2bef8f12d24c295e2b1fa982354dc4c0aee48b07d8bb4a33e6e1eeaf974c3 WHIRLPOOL 8c0bb741b0a074f6b6a8b241f31224985954f46e63329a6c4b3ebd27190a9dcaa361a0269939ac453e2e3fe77917c31e3d06b0752defadebf64ec13a18d57de9
DIST cap3.linux.tar 409600 SHA256 49916f0ac2dc7b6f28fd88e79f98eb097e059839bd9311593ef3fc6f77bc4648 SHA512 3039d5c195b9e0358faf9038378b0a406eac944f7bdf8de8f0cb90e33bd73c6ee72c2f2aea62bfe520ae5a6b25c7c4abf7025d95cd997159092b3f44f513c6c6 WHIRLPOOL d3e5faa33766aca9180d5ebaeb09a580c179a47483468caa1986b7d5e238256335b1f89046c080c57dd5638e398b5273b72733ce395c6000963d3207171863b6
+DIST cap3.linux.x86_64.tar 450560 SHA256 3aff30423e052887925b32f31bdd76764406661f2be3750afbf46341c3d38a06 SHA512 aded71d9e613959d9b5f4326e4c6a7a7e6f6e6b6f0ec9c044e042caf7908bd218a37dcfacf217977d2b3be36425a9057b9d87e192536353be1a311cfbbb0397e WHIRLPOOL 58713649914d5941cb0fed294b9e8d2e431ee62e603af9025485e184243b217c83c8414921a703a2f9f7314bae486b750f47e9bff4069bb1f345ae92f73f4b9b
diff --git a/sci-biology/cap3-bin/cap3-bin-20071221.ebuild b/sci-biology/cap3-bin/cap3-bin-20071015.ebuild
index 987b0e04f..987b0e04f 100644
--- a/sci-biology/cap3-bin/cap3-bin-20071221.ebuild
+++ b/sci-biology/cap3-bin/cap3-bin-20071015.ebuild
diff --git a/sci-biology/cap3-bin/cap3-bin-20150210.ebuild b/sci-biology/cap3-bin/cap3-bin-20150210.ebuild
new file mode 100644
index 000000000..72f7bca0b
--- /dev/null
+++ b/sci-biology/cap3-bin/cap3-bin-20150210.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="CAP3 is for small-scale assembly of EST sequences with or without quality value"
+HOMEPAGE="http://seq.cs.iastate.edu"
+# These exist currently and contain version 20071221:
+# http://seq.cs.iastate.edu/CAP3/cap3.linux.tar
+# http://seq.cs.iastate.edu/CAP3/cap3.linux.i686_xeon64.tar
+# http://seq.cs.iastate.edu/CAP3/cap3.linux.opteron64.tar
+
+# The /pub/ directory is gone although contained same version of binaries but for some different platforms:
+# http://seq.cs.iastate.edu/CAP3/cap3.linux.opteron64.tar
+# http://seq.cs.iastate.edu/CAP3/cap3.linux.i686_xeon64.taran old version (2009)
+
+SRC_URI="
+ x86? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.tar )
+ amd64? ( http://seq.cs.iastate.edu/CAP3/cap3.linux.x86_64.tar )"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+S="${WORKDIR}/CAP3"
+
+src_install() {
+ exeinto /opt/${PN}
+ doexe cap3 formcon
+ dosym ../${PN}/cap3 /opt/bin/cap3
+ dosym ../${PN}/formcon /opt/bin/formcon
+ dodoc README
+ newdoc doc.txt cap3.txt
+ newdoc aceform ACE_file_format.txt
+ # other examples
+ # http://seq.cs.iastate.edu/pub/CAP3/data.tar
+ dodir /usr/share/cap3/examples
+ insinto /usr/share/cap3
+ doins -r example
+}
diff --git a/sci-biology/cd-hit/Manifest b/sci-biology/cd-hit/Manifest
index e3691a860..7bbf8864c 100644
--- a/sci-biology/cd-hit/Manifest
+++ b/sci-biology/cd-hit/Manifest
@@ -1 +1 @@
-DIST cd-hit-v4.6.1-2012-08-27.tgz 652425 SHA256 5e26431892609511992542c39705a1427e2fd6a526241977c527dfc74f795932 SHA512 5c353d151a7999d4ca6864fa9b987493315ed0dc10d64012ada219889f53f317098dbbf7cbff30653a40e4e2953b3b0addaba8fe08895c509e39efe9f8f23d90 WHIRLPOOL 3e5d4432f29da9cc0a300bf1d8d485e42a09bc426ccca7ac8ea0079759a23757171145c2977b07a5a83944c4f2c4e06acccddc1d80e82cd1383c31e1d43cb9bf
+DIST cd-hit-4.6.5.tar.gz 1148585 SHA256 3891497fa81ae67d59fb4dc301740bc21aa3823df792138ab5f2038831faa899 SHA512 d9dbcc61db36c67ccf4fc01f13c5a1a25d246ce60608ba1ac9eb8df4430c92fc70726b8adeaf5cc016025a07aa1d3f675a3636c5439cf3705992753497e319da WHIRLPOOL 3d52f7a12a21aa6b0ca2ae709034bacf1261245fe5c4aa80a707482be3808f5447f23199a013d92ac5aeb2679d0b83df9921b46a8a0a9393cc9094216a7294e6
diff --git a/sci-biology/cd-hit/cd-hit-4.6.1.ebuild b/sci-biology/cd-hit/cd-hit-4.6.1.ebuild
deleted file mode 100644
index aa5180115..000000000
--- a/sci-biology/cd-hit/cd-hit-4.6.1.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils flag-o-matic toolchain-funcs
-
-RELDATE="2012-08-27"
-RELEASE="${PN}-v${PV}-${RELDATE}"
-
-DESCRIPTION="Clustering Database at High Identity with Tolerance"
-HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
-SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-LICENSE="GPL-2"
-IUSE="doc openmp"
-
-S="${WORKDIR}"/${RELEASE}
-
-pkg_setup() {
- use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
-}
-
-src_prepare() {
- tc-export CXX
- use openmp || append-flags -DNO_OPENMP
- epatch "${FILESDIR}"/${PV}-gentoo.patch
-}
-
-src_compile() {
- local myconf=
- use openmp && myconf="openmp=yes"
- emake ${myconf}
-}
-
-src_install() {
- dodir /usr/bin
- emake PREFIX="${ED}/usr/bin" install
- dodoc ChangeLog
- use doc && dodoc doc/*
-}
diff --git a/sci-biology/cd-hit/cd-hit-4.6.5.ebuild b/sci-biology/cd-hit/cd-hit-4.6.5.ebuild
new file mode 100644
index 000000000..7d6686abf
--- /dev/null
+++ b/sci-biology/cd-hit/cd-hit-4.6.5.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+RELDATE="2016-03-04"
+RELEASE="${PN}-v${PV}-${RELDATE}"
+
+DESCRIPTION="Clustering Database at High Identity with Tolerance"
+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit
+ http://weizhongli-lab.org/cd-hit"
+SRC_URI="https://github.com/weizhongli/cdhit/archive/V${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+LICENSE="GPL-2"
+IUSE="doc openmp"
+
+DEPEND="!sci-biology/cd-hit-auxtools"
+
+S="${WORKDIR}"/cdhit-"${PV}"
+
+pkg_setup() {
+ use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
+}
+
+src_prepare() {
+ tc-export CXX
+ use openmp || append-flags -DNO_OPENMP
+ epatch "${FILESDIR}"/${PV}-gentoo.patch
+}
+
+src_compile() {
+ local myconf=
+ use openmp && myconf="openmp=yes"
+ emake ${myconf}
+ cd cd-hit-auxtools || die
+ emake ${myconf}
+}
+
+src_install() {
+ dodir /usr/bin
+ emake PREFIX="${ED}/usr/bin" install
+ dobin psi-cd-hit/*.pl cd-hit-auxtools/*.pl cd-hit-auxtools/{cd-hit-lap,read-linker,cd-hit-dup}
+ dodoc ChangeLog psi-cd-hit/README.psi-cd-hit
+ use doc && dodoc doc/* psi-cd-hit/qsub-template "${FILESDIR}"/cd-hit-auxtools-manual.txt
+}
+
+pkg_postinst(){
+ einfo "From the original http://weizhong-lab.ucsd.edu/software/cdhit-454 package"
+ einfo "we still lack cdhit-cluster-consensus part. You may want to install yourself"
+ einfo "http://weizhong-lab.ucsd.edu/softwares/cd-hit-454/cdhit-cluster-consensus-2013-03-27.tgz"
+ einfo ""
+ einfo "The cd-hit-auxtools are no longer a separate package and belong to cd-hit since"
+ einfo "version 4.6.5. However, there is no manual for that in current cd-hit tree. Therefore"
+ einfo "see http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit-auxtools-manual"
+ einfo "A local copy is is in /usr/share/doc/${PN}/cd-hit-auxtools-manual.txt"
+}
diff --git a/sci-biology/cd-hit/files/4.6.1-gentoo.patch b/sci-biology/cd-hit/files/4.6.5-gentoo.patch
index d9db28ca8..5e989da40 100644
--- a/sci-biology/cd-hit/files/4.6.1-gentoo.patch
+++ b/sci-biology/cd-hit/files/4.6.5-gentoo.patch
@@ -1,6 +1,6 @@
---- Makefile.ori 2014-06-01 20:12:44.000000000 +0200
-+++ Makefile 2014-06-01 20:16:34.000000000 +0200
-@@ -1,16 +1,13 @@
+--- Makefile.ori 2016-02-12 01:58:32.000000000 +0100
++++ Makefile 2016-03-15 16:55:53.726069350 +0100
+@@ -1,7 +1,4 @@
-
-CC = g++ -Wall -ggdb
-CC = g++ -pg
@@ -8,27 +8,28 @@
+CXX ?= g++
# without OpenMP
--CCFLAGS = -DNO_OPENMP
-+#CXXFLAGS = -DNO_OPENMP
- # with OpenMP
+@@ -9,9 +6,9 @@
# in command line:
# make openmp=yes
- ifeq ($(openmp),yes)
--CCFLAGS = -fopenmp
-+CXXFLAGS += -fopenmp
+ ifeq ($(openmp),no)
+- CCFLAGS = -DNO_OPENMP
++ CXXFLAGS += -DNO_OPENMP
+ else
+- CCFLAGS = -fopenmp
++ CXXFLAGS += -fopenmp
endif
# support debugging
-@@ -18,17 +15,17 @@
+@@ -19,13 +16,13 @@
# make debug=yes
# make openmp=yes debug=yes
ifeq ($(debug),yes)
-CCFLAGS += -ggdb
-+CXXFLAGS +=
++CXXFLAGS += -ggdb
else
-CCFLAGS += -O2
-+CXXFLAGS +=
++CXXFLAGS ?= -O2
endif
ifdef MAX_SEQ
@@ -37,13 +38,12 @@
endif
#LDFLAGS = -static -o
--LDFLAGS += -o
-+#LDFLAGS += -o
-
+@@ -34,10 +31,10 @@
PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
-@@ -36,7 +33,7 @@
- CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS)
+ # Propagate hardening flags
+-CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS)
++CXXFLAGS := $(CPPFLAGS) $(CXXFLAGS)
.c++.o:
- $(CC) $(CCFLAGS) -c $<
@@ -51,32 +51,32 @@
all: $(PROGS)
-@@ -46,49 +43,49 @@
+@@ -47,49 +44,49 @@
# programs
cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit
++ $(CXX) $(CXXFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d
++ $(CXX) $(CXXFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est
++ $(CXX) $(CXXFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d
++ $(CXX) $(CXXFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div
++ $(CXX) $(CXXFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
- $(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
-+ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454
++ $(CXX) $(CXXFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
# objects
cdhit-common.o: cdhit-common.c++ cdhit-common.h
@@ -112,7 +112,52 @@
+ $(CXX) $(CXXFLAGS) cdhit-454.c++ -c
-PREFIX ?= /usr/local/bin
-+PREFIX ?= $(DESTDIR)/usr/bin
++PREFIX ?= $(DESTDIR)/usr/local/bin
install:
for prog in $(PROGS); do \
+--- cd-hit-auxtools/Makefile.ori 2016-03-15 17:02:39.986070411 +0100
++++ cd-hit-auxtools/Makefile 2016-03-15 17:05:00.556070779 +0100
+@@ -1,9 +1,8 @@
++CXX ?= g++
+
+-CC = g++
+-
+-CFLAGS = -Wall -Wno-unused -I. -Imintlib
++CXXFLAGS ?= -Wall -Wno-unused
+ LFLAGS = -fPIC
+-
++CPPFLAGS = -I. -Imintlib
+
+ UNAME = $(shell uname)
+
+@@ -18,7 +17,7 @@
+ ifeq ($(debug),yes)
+ CXXFLAGS += -ggdb
+ else
+-CFLAGS += -O2
++CXXFLAGS ?= -O2
+ endif
+
+
+@@ -32,16 +31,16 @@
+ .SUFFIXES: .c .obj .cpp .cc .cxx .C
+
+ .cxx.o:
+- $(CC) -c $(CFLAGS) -o $@ $<
++ $(CXX) -c $(CXXFLAGS) $(CPPFLAGS) -o $@ $<
+
+ cd-hit-dup: $(OBJECTS) cdhit-dup.o
+- $(CC) $(LFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup
++ $(CXX) $(CXXFLAGS) $(LFLAGS) $(OBJECTS) cdhit-dup.o -o cd-hit-dup
+
+ cd-hit-lap: $(OBJECTS) cdhit-lap.o
+- $(CC) $(LFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap
++ $(CXX) $(CXXFLAGS) $(LFLAGS) $(OBJECTS) cdhit-lap.o -o cd-hit-lap
+
+ read-linker: $(OBJECTS) read-linker.o
+- $(CC) $(LFLAGS) $(OBJECTS) read-linker.o -o read-linker
++ $(CXX) $(CXXFLAGS) $(LFLAGS) $(OBJECTS) read-linker.o -o read-linker
+
+ clean:
+ rm $(OBJECTS) cdhit-dup.o cdhit-lap.o read-linker.o
diff --git a/sci-biology/cd-hit/files/cd-hit-auxtools-manual.txt b/sci-biology/cd-hit/files/cd-hit-auxtools-manual.txt
new file mode 100644
index 000000000..6e0ca68a9
--- /dev/null
+++ b/sci-biology/cd-hit/files/cd-hit-auxtools-manual.txt
@@ -0,0 +1,212 @@
+http://weizhong-lab.ucsd.edu/cd-hit/wiki/doku.php?id=cd-hit-auxtools-manual
+
+CD-HIT AuxTools: Manual
+
+Last updated: 2012/03/08 00:59
+
+http://cd-hit.org
+
+http://bioinformatics.org/cd-hit/
+
+Program developed by Weizhong Li's lab at UCSD http://weizhong-lab.ucsd.edu liwz@sdsc.edu
+Introduction
+
+CD-HIT AuxTools is a set of auxiliary programs that can be used to assist the analysis of the next generation sequencing data. It currently includes programs for removing read duplicates, finding pairs of overlapping reads or joining pair-end reads etc.
+cd-hit-dup
+
+cd-hit-dup is a simple tool for removing duplicates from sequencing reads, with optional step to detect and remove chimeric reads. A number of options are provided to tune how the duplicates are removed. Running the program without arguments should print out the list of available options, as the following:
+
+Options:
+ -i Input file;
+ -i2 Second input file;
+ -o Output file;
+ -d Description length (default 0, truncate at the first whitespace character)
+ -u Length of prefix to be used in the analysis (default 0, for full/maximum length);
+ -m Match length (true/false, default true);
+ -e Maximum number/percent of mismatches allowed;
+ -f Filter out chimeric clusters (true/false, default false);
+ -s Minimum length of common sequence shared between a chimeric read
+ and each of its parents (default 30, minimum 20);
+ -a Abundance cutoff (default 1 without chimeric filtering, 2 with chimeric filtering);
+ -b Abundance ratio between a parent read and a chimeric read (default 1);
+ -p Dissimilarity control for chimeric filtering (default 1);
+
+Option details
+Common options
+
+Here are the more detailed description of the options.
+
+ -i Input file;
+
+Input file that must be in fasta or fastq format.
+
+ -i2 Second input file;
+
+cd-hit-dup can take a pair of files as inputs, assuming they contain sequences of pair-end reads. ”-i” can be used to specify the file for the first end; and ”-i2” can be used to specify the file for the second end.
+
+When two files of pair-end reads are used as inputs, each pair of reads will be concatenated into a single one. And the following steps of duplicate and chimeric detection and removing.
+
+ -o Output file;
+
+Output file which contains a list of reads without duplicates.
+
+ -d Description length (default 0, truncate at the first whitespace character)
+
+The length of description line that should be written to the output.
+
+ -u Length of prefix to be used in the analysis (default 0, for full/maximum length);
+
+For pair-end inputs, the program will take part (whole or prefix) of the first end and part (whole or prefix) of the second read, and join them together to form a single read to do the analysis. A positive value of this option specifies the length of the prefix to be taken from each read. If a read is shorter than this length, letter 'N's will be appended to the read to make up for the length. When this option is not used or is used with a non-positive value, the program will use the length of the longest read as the value of this option.
+
+For single input analysis, only a positive value of this option will be effective. It also allows the program to use only the prefix up to the specified length of each read to do the analysis. In case that a read is shorter than this length, no 'N' is appended to the read since it is not necessary.
+Options for duplicate detection
+
+ -m Match length (true/false, default true);
+
+”-m” specifies whether the lengths of two reads should be exactly the same to be considered as duplicates.
+
+ -e Maximum number/percent of mismatches allowed;
+
+Maximum number/percent of mismatches can be specified to control the similarity between two reads for duplicate and chimeric detection. For duplicate detection, any two reads with number of mismatches no greater than the specified value are considered to be duplicates. For chimeric detection, this option control how similar a read should be to either of its parents.
+Options for chimeric filtering
+
+ -f Filter out chimeric clusters (true/false, default false);
+
+This option specifies whether or not to carry out an additional step to filter out chimeric clusters.
+
+ -s Minimum length of common sequence shared between a chimeric read
+ and each of its parents (default 30, minimum 20);
+
+A read or cluster representative is considered as a potential chimeric only if it shares at least the number of bases specified by this option with either of its parents. This option is effective only if the option is set to true for filtering chimeric clusters.
+
+ -a Abundance cutoff (default 1 without chimeric filtering, 2 with chimeric filtering);
+
+Each read is associated with an abundance number, which is the number of duplicates for the read. cd-hit-dup always assumes the input contains duplicates and perform the duplicate detection step. If no duplicate is found, the input is assumed to have duplicates remove in advance, and then, the program will try to obtain the abundance information from the descriptions of the reads, it interprets the number following “_abundance_” as the abundance number.
+
+The abundance cutoff is mainly used for chimeric filtering to skip chimeric checking on reads with abundance below this cutoff.
+
+ -b Abundance ratio between a parent read and a chimeric read (default 1);
+
+This option specifies the abundance ratio between a parent read and a chimeric read. So for a read to be chimeric, either of its parents must have abundance at least as high as the ratio times the abundance of the chimeric read.
+
+ -p Dissimilarity control for chimeric filtering (default 1);
+
+Internally dissimilarity is measured by percent of mismatches with ungapped alignments. By default the percentage cutoff is set to 0.01 (one percent). This option specifies a multiplier to this percentage cutoff. A higher value will increase the dissimilarity thresholds in chimeric filtering.
+Output files
+
+cd-hit-dup will output three files. Two of them are the same as the output files of CD-HIT: one (named exactly the same as the file name specified by the ”-o” option) is the cluster (or duplicate) representatives, the other is the clustering file (xxx.clstr) relating each duplicate to its representative. The third file (xxx2.clstr) contains the chimeric clusters. In this file, the description for each chimeric cluster contains cluster ids of its parent clusters from the clustering file xxx.clstr.
+Examples
+Duplicate Detection
+
+Remove duplicates using default parameters:
+
+cd-hit-dup -i input.fa -o output
+
+By default, only reads that are identical are considered as duplicates. If ”-m” is set to false, duplicates will be allowed to have different length, but the longer ones must have a prefix that is identical to the shorter ones.
+
+Remove duplicates with a few mismatches:
+
+cd-hit-dup -i input.fa -o output -e 2
+cd-hit-dup -i input.fa -o output -e 0.01
+
+The former will allow each duplicate read to have up to 2 mismatches when aligned to its representative; and the later will allow up to one percent mismatches.
+
+Remove duplicates from pair-end reads:
+
+cd-hit-dup -i pair-end1.fa -i2 pair-end2.fa -o output
+
+Each read from “pair-end1.fa” and “pair-end2.fa” will be joint to form a single read to detect duplicates. If they all are of the same length, the full length of each ends will be used in forming the single read; otherwise, the default value of option ”-u” will be used to determine how the single read is created.
+
+Remove duplicates from pair-end reads with control on how the pair-ends are jointed:
+
+cd-hit-dup -i pair-end1.fa -i2 pair-end2.fa -o output -u 100
+
+With explicit ”-u” options, any reads shorter than 100 will be padded with 'N's, and the longer ones will be cut down to 100 base long. Then each pair of the 100 base long reads will be jointed to form a single 200 base long read.
+Chimeric Filtering
+
+cd-hit-dup offers a very efficient way to detect chimeric reads. The basic idea is to find two parent reads whose cross-over is sufficient similar to the chimeric read, while each single parent is sufficiently dissimilar to it.
+
+Such dissimilarity is measured by the percent of mismatches for no-gapped alignments. For a given percentage “p” (from option ”-p”), a chimeric read must share at least “p” percent mismatches with any other single read, namely, it much be sufficiently dissimilar to any single read.
+
+For more robust detection of chimeric reads, a background percentage “p_bg” is calculated as the mismatch percentage shared between the candidate chimeric read and the single read that is most similar to the candidate. If “p_bg” is greater than “1.5*p”, “1.5*p” will be used as “p_bg” instead.
+
+For a read to be classified as chimeric read, there must exist two reads/parents such that, the leading part of the read is sufficiently similar to one parent, and the rest is sufficiently similar to the other parent, with at most “p+p_bg” percent of mismatches in each part. And the crossover between the two parents must share at most “p_bg” mismatches with the chimeric read.
+
+Chimeric filtering with default parameters:
+
+cd-hit-dup -i input.fa -o output -f true
+
+Chimeric filtering with specified similarity level:
+
+cd-hit-dup -i input.fa -o output -f true -p 1.5
+
+Chimeric filtering with specified abundance difference:
+
+cd-hit-dup -i input.fa -o output -f true -a 2
+
+which means each parent of a chimeric read must be a least as twice abundant as the chimeric read.
+
+Chimeric filtering will produce a cluster file named like “xxx2.clstr”, in which each cluster entry is a chimeric read/cluster. For example,
+
+......
+>Cluster 4 chimeric_parent1=2,chimeric_parent2=8
+0 256nt, >FV9NWLF01CRIR3_abundance_23... *
+>Cluster 5 chimeric_parent1=2,chimeric_parent2=0
+0 250nt, >FV9NWLF01B4TBX_abundance_21... *
+......
+
+here “Cluster 5” contains a chimeric read “FV9NWLF01B4TBX”, whose parents are identified by cluster numbers “2” and “0” from the associated “xxx.clstr” file,
+
+>Cluster 0
+0 252nt, >FV9NWLF01ANLX2_abundance_2239... *
+>Cluster 1
+0 246nt, >FV9NWLF01C3KOB_abundance_1465... *
+>Cluster 2
+0 260nt, >FV9NWLF01AQOWA_abundance_1284... *
+......
+
+So the parent reads of the chimeric read “FV9NWLF01B4TBX” are “FV9NWLF01AQOWA” and “FV9NWLF01ANLX2”.
+cd-hit-lap
+
+cd-hit-lap is program for extracting pairs of overlapping reads by clustering based on tail-head overlaps (with perfect matching). The basic clustering strategy is the same as that in standard CD-HIT programs. In this program, each read is clustered as either a “representative” or a “redundant” read. For each “redundant” read, it must have a prefix that is identical a suffix of its representative read.
+
+The options of this program can be obtained by running it it without any arguments:
+
+[compute-0-0 cdhit-dup]$ ./cd-hit-lap
+Options:
+ -i Input file;
+ -o Output file;
+ -m Minimum length of overlapping part (default 20);
+ -p Minimum percentage of overlapping part (default 0, any percentage);
+ -d Description length (default 0, truncate at the first whitespace character)
+ -s Random number seed for shuffling (default 0, no shuffling; shuffled before sorting by length);
+ -stdout Standard output type (default "log", other options "rep", "clstr");
+
+The two options ”-m” and ”-p” can be used to control the minimum overlap that is required to classify them as overlapping reads. Each pair of overlapping reads must have overlap length no less than the threshold specified by ”-m”, and must also not be less than the length threshold computed from the ”-p” option.
+
+Since the overlapping reads are searched using a greedy strategy, so different sortings of reads may lead to different result. So it is advisable to run the program multiple times with read shuffling by different random number seeds, and then collect and merge the results.
+
+Sometimes it may be more convenient to pipe the results of this program as stdout directly to the stdin of other programs, to do this, the option ”-stdout” can be used to choose which type (“log” for program console information, “rep” for representative reads in FASTA or FASTQ format, “clstr” for the clustering output in CD-HIT format) of results to be writen to the stdout.
+
+The output format of this program is the same as the standard CD-HIT. In the .clstr file, the alignment positions indicate how the reads are overlapped. For example,
+
+>Cluster 0
+0 75nt, >1_lane2_624... *
+1 75nt, >1_lane2_7169... at 1:65:11:75/+/100.00%
+2 75nt, >1_lane2_36713... at 69:1:1:69/-/100.00%
+3 75nt, >1_lane2_141482... at 1:56:20:75/+/100.00%
+
+The cluster member #0 in cluster #0 is the representative of the cluster, and it overlaps with each of the other members in the cluster. For cluster member #1, “1:65:11:75/+” tells that the first 65 bases of member #1 overlaps with the last 65 bases of member #0; “69:1:1:69/-” indicates that the last 69 bases of member #2 overlaps with the first 69 bases of member #0.
+read-linker
+
+read-linker is a very simple program to concatenate pair-end reads into single ones. It support the following options:
+
+[compute-0-0 cdhit-dup]$ ./read-linker
+Options:
+ -1 file Input file, first end;
+ -2 file Input file, second end;
+ -o file Output file;
+ -l number Minimum overlapping length (default 10);
+ -e number Maximum number of errors (mismatches, default 1);
+
+Only the pairs of reads that share at least a minimum overlapping length with mismatched no more than the maximum number of errors, are jointed to form a single read.
diff --git a/sci-biology/cg-cat/cg-cat-20150130.ebuild b/sci-biology/cg-cat/cg-cat-20150130.ebuild
index af9a76a45..af5e73184 100644
--- a/sci-biology/cg-cat/cg-cat-20150130.ebuild
+++ b/sci-biology/cg-cat/cg-cat-20150130.ebuild
@@ -13,20 +13,26 @@ SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/d
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
IUSE=""
-DEPEND=">=virtual/jre-1.6:*"
-RDEPEND="${DEPEND}"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.6:*
+ dev-lang/perl
+ sci-biology/ncbi-tools"
+DEPEND="${RDEPEND}
+ >=virtual/jdk-1.6:*
+ dev-java/ant-core"
S="${WORKDIR}"/r2cat
src_prepare(){
- sed -e "s#/vol/bioapps#"${D}"/usr#" -e "s#/vol/bibidev/r2cat#"${D}"/usr#" -i Makefile
+ sed -e "s#/vol/bioapps#"${D}"/usr#" -e "s#/vol/bibidev/r2cat#"${D}"/usr#" -i Makefile || die
+ sed -e "s#/vol/gnu#/usr#" -i de/bielefeld/uni/cebitec/r2cat/blast_to_r2cat.pl || die
}
src_compile(){
- emake
+ emake r2cat.jar
}
src_install(){
@@ -35,9 +41,20 @@ src_install(){
# Enter Passphrase for keystore: jarsigner: you must enter key password
# Makefile:44: recipe for target 'cg-cat.jar' failed
mkdir -p "${D}"/usr/share/r2cat
- emake install_cebitec
- emake install_bibiserv
+ # emake install_cebitec
+ # emake install_bibiserv
+ # the blast_to_r2cat.pl script needs bioperl
+ dobin de/bielefeld/uni/cebitec/r2cat/blast_to_r2cat.pl
+ java-pkg_dojar r2cat.jar || die
+ dodoc README.md ReadmeLicenses.txt
+ insinto /usr/share/doc/"${PN}"/html
+ doins de/bielefeld/uni/cebitec/r2cat/help/*
}
-# java -Xmx1024M -jar r2cat.jar
-# java -Xmx1024M -cp r2cat.jar de.bielefeld.uni.cebitec.treecat.Treecat -Xmx -d64
+# to start r2cat:
+# java -Xmx10240M -jar r2cat.jar de.bielefeld.uni.cebitec.r2cat.R2cat
+
+# to start treecat:
+# java -Xmx10240M -cp r2cat.jar de.bielefeld.uni.cebitec.treecat.Treecat -Xmx -d64
+
+# add -d64 on the java commandline if you need more than 4GB of memory and your system can handle it
diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
index 46144771b..002e0074b 100644
--- a/sci-biology/consed/consed-29.ebuild
+++ b/sci-biology/consed/consed-29.ebuild
@@ -22,6 +22,7 @@ DEPEND=">=x11-libs/motif-2.3:0"
# This file was about sci-biology/samtools-1.2 time moved to sci-libs/htslib-1.2.1
RDEPEND="${DEPEND}
<sci-biology/samtools-1.0
+ >=sci-biology/samtools-0.1.18
>=sci-biology/phred-000925
>=sci-biology/phrap-1.080721
dev-lang/perl"
@@ -48,12 +49,12 @@ src_prepare() {
-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/ -I/usr/include/htslib/#' "${S}/makefile" || die
sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
sed \
- -e 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' \
+ -e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \
-i "${S}"/scripts/* || die
}
src_compile() {
- einfo "consed does not compile with sys-devel/gcc-4.6:* or newer (but 4.4.7 works)"
+ einfo "consed does not compile with >=sys-devel/gcc-4.6:* but 4.4.7 works"
default
emake -C misc/mktrace
emake -C misc/phd2fasta
@@ -70,10 +71,9 @@ src_install() {
standard polyphred autofinish assembly_view 454_newbler \
align454reads align454reads_answer solexa_example \
solexa_example_answer selectRegions selectRegionsAnswer
- echo 'CONSED_HOME="${EPREFIX}/usr"' > "${S}"/99consed || die
- echo 'CONSED_PARAMETERS="${EPREFIX}/etc/consedrc"' >> "${S}"/99consed || die
- mkdir -p "${ED}"/etc/consedrc || die
- touch "${ED}"/etc/consedrc || die
+ echo CONSED_HOME="${EPREFIX}"/usr > "${S}"/99consed || die
+ echo CONSED_PARAMETERS="${EPREFIX}"/etc/consedrc >> "${S}"/99consed || die
+ touch "${ED}"/etc/consedrc || die "Cannot create a file for system-wide settings"
doenvd "${S}/99consed"
sed \
-e "s#/usr/local/genome#${EPREFIX}/usr#" \
diff --git a/sci-biology/cross_genome/cross_genome-20140822.ebuild b/sci-biology/cross_genome/cross_genome-20140822.ebuild
index 1a290766d..eca7e195d 100644
--- a/sci-biology/cross_genome/cross_genome-20140822.ebuild
+++ b/sci-biology/cross_genome/cross_genome-20140822.ebuild
@@ -6,7 +6,7 @@ EAPI=6
DESCRIPTION="Genome scaffolding using cross-species synteny"
HOMEPAGE="http://www.sanger.ac.uk/science/tools/crossgenome"
-SRC_URI="https://sourceforge.net/projects/phusion2/files/cross_genome/cross_genome.tar.gz -> cross_genome-20140822.tar.gz"
+SRC_URI="https://sourceforge.net/projects/phusion2/files/cross_genome/cross_genome.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3+"
SLOT="0"
diff --git a/sci-biology/cutadapt/Manifest b/sci-biology/cutadapt/Manifest
index 03806c013..b2beaff1e 100644
--- a/sci-biology/cutadapt/Manifest
+++ b/sci-biology/cutadapt/Manifest
@@ -1,3 +1 @@
-DIST cutadapt-1.2.1.tar.gz 104440 SHA256 1baf91c7351ee3464cd01a7f767fe474675ab1b1f7bb110ffe3722e8126ed5cf SHA512 5cd48f342ed75d18780ec63c73f2c42d239253d8dded3161c39f7a26e915f195055c8c4097305246a1418f8b4d3c8853adc1074cbe2a9c1a1b0af644e36771b6 WHIRLPOOL b5c6ceb65be0fcfe418b31cb4c2f8b427d017f71eed182585dc4353079df21ba2ae16354bb6cfcc17bfb39d155ae87fc97fed55b3d0f6ebc68197d98c395c31e
-DIST cutadapt-1.4.1.tar.gz 152401 SHA256 841159772863d9e23647884075e9b12ff284d0942a926be3016c841f2348b6b3 SHA512 1e327f1ee52c7084f4ee986181322278cf03163b483d4deeba721ec606804304dea2770b816a876e5fc280ab960f03c03e57ae7ed83856dc0c25d1ee272862c9 WHIRLPOOL e7db7e3155fa04dd49186edf25aeb483f91405e70fbbf7711d23ca8f6d7c815bea06718d516535e3236847260208542caccf14aa23c7d184ac3ddcde8ff13dc7
-DIST cutadapt-1.5.tar.gz 364322 SHA256 6d06c2d2c03620913ded530c60ef6fa20fcad4ed987b1d1f0a5e7c24e2ddec83 SHA512 8f7c5ccc847a462a0d00b68884e000c6179d38654e247d5782a7d1e779a6d1cbc66df3a677396df345ee74235c20bb2655731c73b4150caf81d058939b774d7c WHIRLPOOL 68df9c44f4b7ff8bea1dd9284b774924ca8409aa4fcbd1895e6f1ae461cd9b004216e48592feb3590a81cadcdc238d1bab7d75a3306dfc2a4dbbfc69bd906ae2
+DIST cutadapt-1.9.1.tar.gz 595412 SHA256 a83d24455109be6426ee8de75d906d2b82cc9d59e2e86e0c2b465d3cacb94675 SHA512 9611f3f12e2c99bf03cca2e921e030cafd91782b40e1204e5dc44e4f8b910e2248ddec7e8d394b40460348e8f195ed4fcebc48c018320ce2c3daa1d1722f39c5 WHIRLPOOL 27b4d4724d96d8b2a56e3535ed7b1451afa2fd2f01a22cc09aa5f49b017a82849f94155e05424dae3a5a98a5f24f7dc28ad4ce86467e7adc1283fc3ca0aa5942
diff --git a/sci-biology/cutadapt/cutadapt-1.4.1.ebuild b/sci-biology/cutadapt/cutadapt-1.4.1.ebuild
deleted file mode 100644
index 46b60719e..000000000
--- a/sci-biology/cutadapt/cutadapt-1.4.1.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
-HOMEPAGE="https://code.google.com/p/cutadapt/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
diff --git a/sci-biology/cutadapt/cutadapt-1.5.ebuild b/sci-biology/cutadapt/cutadapt-1.5.ebuild
deleted file mode 100644
index 46b60719e..000000000
--- a/sci-biology/cutadapt/cutadapt-1.5.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
-HOMEPAGE="https://code.google.com/p/cutadapt/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
diff --git a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild b/sci-biology/cutadapt/cutadapt-1.9.1.ebuild
index 46b60719e..ee91f3cec 100644
--- a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
+++ b/sci-biology/cutadapt/cutadapt-1.9.1.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python2_7 )
inherit distutils-r1
DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
-HOMEPAGE="https://code.google.com/p/cutadapt/"
+HOMEPAGE="https://github.com/marcelm/cutadapt"
SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
diff --git a/sci-biology/cutadapt/cutadapt-9999.ebuild b/sci-biology/cutadapt/cutadapt-9999.ebuild
index 46c2382b8..213ea8506 100644
--- a/sci-biology/cutadapt/cutadapt-9999.ebuild
+++ b/sci-biology/cutadapt/cutadapt-9999.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python2_7 )
inherit distutils-r1 git-r3
DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
-HOMEPAGE="https://code.google.com/p/cutadapt/"
+HOMEPAGE="https://github.com/marcelm/cutadapt"
EGIT_REPO_URI="https://github.com/marcelm/cutadapt"
LICENSE="MIT"
diff --git a/sci-biology/exomiser-bin/Manifest b/sci-biology/exomiser-bin/Manifest
index 6e50d183b..67ae9e248 100644
--- a/sci-biology/exomiser-bin/Manifest
+++ b/sci-biology/exomiser-bin/Manifest
@@ -1 +1,3 @@
-DIST exomiser-cli-7.0.0.BETA-distribution.zip 1243391234 SHA256 524f98ef38e1cf958fcaca3bada78f52f1053905c97fd0659d92eb470474df2b SHA512 68f9e71599ab42f4500da0559ab5d1893245a2908ece245425342a9e855258de539ba440ff5c56c9c22485f646483d4b517b1cf30ba985a1ac39e6e4047a01e5 WHIRLPOOL 6eebe7b9d54af91d851d50f00229885063e8d1f6dd2ecba4624ffec5e8898aa1465f2f4043dccda1af039557ab5e4b8467d6c78a689a8b63149b5f569ff96021
+DIST exomiser-bin.README 1445 SHA256 bf9b6ad3a0cd56fbe9d8155b5d671c1ce31b70742eef116a6158af4c9cebc488 SHA512 db27fbe1d7550ddde090b96928ff9c01049e2dbdee3927c73fff6810f5c5d921738866bf11424fddc14b5c955d79f7e9e6c6899191dc53e58d221388259800f8 WHIRLPOOL e0dff092281e5fae36c96f2af01d40e0a614acc4f638e80db2471743b0a61cff8629fa611a54271ba56db347ea416b6183a746294e29d7eb1f55db747f57942f
+DIST exomiser-bin.README.md 9604 SHA256 262565653c4c4ede6872b6f2b174266ef39f05b4ef72048028f939a7df0050d6 SHA512 e6f9eb9114ef875e6e471eda1cb9118d725bd9ec4c1fbcc2cd0ee63069768816a98a4de03529f10f865837c8b9efe4e4c525b5e2471e44440f355a814bb82891 WHIRLPOOL 0ada5a7663fb98bdf778aa0c85f2b4d70eb0250934556d3001c0545776c4e23a74400688205042b60a8c5c0d965f6f15159279a262949ce2c3e355d67719eec4
+DIST exomiser-cli-7.2.1-distribution.zip 51146162 SHA256 4a89fcfe7ce80fe057b4db1cbb07e9fadc8f05d57bd3e95756b4d6e2a3b9148e SHA512 1d523e6e8de4b03f1271ff9eb29397f43829e0930934447a77339d5934836a27aeee5c74aeb5e0c9c7acb98e7db07eecd8abb8b163bd845b69e015c784c8ba86 WHIRLPOOL b6031d0887125ed4d257ec855ae074610b6d362f24a88f4b8157282c3a90db9c28913091a2bf2482e304cef1443871321d2b2a2d6ebb818c26a33ff7a1645816
diff --git a/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild b/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild
deleted file mode 100644
index c58cabfae..000000000
--- a/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-DESCRIPTION="Annotate VCF files from whole-exome sequencing (Jannovar, UCSC KnownGenes, hg19)"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/exomiser"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-${PV}.BETA-distribution.zip"
-# 1.16GB !
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sci-biology/Jannovar-bin"
-RDEPEND="${DEPEND}"
-
-pkg_postinst(){
- einfo "Please download 3.7GB file from ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/h2_db_dumps/exomiser-${PV}.BETA.h2.db.gz"
- einfo "and follow README.md"
-}
diff --git a/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild b/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild
new file mode 100644
index 000000000..1346fd2ee
--- /dev/null
+++ b/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Annotate VCF files and prioritize genome/exome mutations (Jannovar, UCSC KnownGenes, hg19)"
+HOMEPAGE="http://www.sanger.ac.uk/science/tools/exomiser"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-${PV}-distribution.zip
+ ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/GenomiserREADME -> ${PN}.README
+ ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/README.md -> ${PN}.README.md"
+# 1.16GB !
+
+LICENSE="AGPL-3+"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/Jannovar-bin"
+RDEPEND="${DEPEND}"
+
+src_install(){
+ dodoc "${DISTDIR}"/${PN}.README "${DISTDIR}"/${PN}.README.md
+}
+
+pkg_postinst(){
+ einfo "Please download 3.7GB file from ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/h2_db_dumps/exomiser-${PV}.BETA.h2.db.gz"
+ einfo "and follow README.md"
+ einfo "The is also 19GB file ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-7.2.1-data.zip"
+ einfo "with test data"
+}
diff --git a/sci-biology/fgap-bin/Manifest b/sci-biology/fgap-bin/Manifest
new file mode 100644
index 000000000..c798ff8d2
--- /dev/null
+++ b/sci-biology/fgap-bin/Manifest
@@ -0,0 +1 @@
+DIST FGAP_1_8_1_LINUX64b.tar.gz 19403911 SHA256 12d824390efddeff5c92c7ea1b191303e46dd9f6b34f2c858a747aaf00f986ef SHA512 fc8d626d158ef362b5aa5d8ef5ffb8840b1496ecb2f4714441d74bc3fca5eacac3eab1e6d93e4344b175eece2b8228d98794493c7d5d300fbb30a8a3b6b8afd0 WHIRLPOOL a44f769771a3d7966ec4633718821281b1715fb63cfd96d5749e655d124d32350376aea88c64fb80cfa8649f30479c48588e9e76eb4334c83069081bfdb40412
diff --git a/sci-biology/fgap-bin/fgap-bin-1.8.1.ebuild b/sci-biology/fgap-bin/fgap-bin-1.8.1.ebuild
new file mode 100644
index 000000000..cb3f72d4f
--- /dev/null
+++ b/sci-biology/fgap-bin/fgap-bin-1.8.1.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Tool to close gaps in de novo assembled contigs or scaffolds"
+HOMEPAGE="http://www.bioinfo.ufpr.br/fgap"
+SRC_URI="https://sourceforge.net/projects/fgap/files/FGAP_1_8_1_LINUX64b.tar.gz"
+# http://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-7-371
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# Matlab (R2012a) or Octave (3.6.2)
+#
+# Source code (Octave/Matlab): https://sourceforge.net/projects/fgap/files/fgap.m
+
+# MATLAB Component Runtime v7.17: https://sourceforge.net/projects/fgap/files/MCR_LINUX64b.tar.gz
+# http://www.mathworks.com/products/compiler/mcr/index.html
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/ncbi-tools+"
diff --git a/sci-biology/fgap-bin/metadata.xml b/sci-biology/fgap-bin/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/fgap-bin/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/fgap/Manifest b/sci-biology/fgap/Manifest
new file mode 100644
index 000000000..c6e88321a
--- /dev/null
+++ b/sci-biology/fgap/Manifest
@@ -0,0 +1 @@
+DIST fgap.m 66256 SHA256 9fdfeccb28ed8461696e05e5cdea32ee63eaead9f0d9c81cf8fe0dc6e59683b8 SHA512 05b0d46eb5a9b3a34e16c045966c58f52bdf09ee2f8c62198338b2d57835815a2ac034b596d6c180733b91edcc012fb77852c8bc0523174251a2c1b3c71b1e27 WHIRLPOOL 623df6b1d2b540fac5d5303e8c08d27128d44dbd678a4e85d49b5304ffde008562c3d4df1996f30d36a4da77f28a09f0c0ae47ee945bb3000fee7f1ffac70921
diff --git a/sci-biology/fgap/fgap-1.8.1.ebuild b/sci-biology/fgap/fgap-1.8.1.ebuild
new file mode 100644
index 000000000..fc5245bc4
--- /dev/null
+++ b/sci-biology/fgap/fgap-1.8.1.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Tool to close gaps in de novo assembled contigs or scaffolds"
+HOMEPAGE="http://www.bioinfo.ufpr.br/fgap"
+SRC_URI="https://sourceforge.net/projects/fgap/files/fgap.m"
+# http://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-7-371
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# Matlab (R2012a) or Octave (3.6.2)
+#
+# Source code (Octave/Matlab): https://sourceforge.net/projects/fgap/files/fgap.m
+
+# MATLAB Component Runtime v7.17: https://sourceforge.net/projects/fgap/files/MCR_LINUX64b.tar.gz
+# http://www.mathworks.com/products/compiler/mcr/index.html
+DEPEND=""
+RDEPEND="${DEPEND}
+ >=sci-biology/ncbi-tools-2.2.28
+ >=sci-mathematics/octave-3.6.2"
diff --git a/sci-biology/fgap/metadata.xml b/sci-biology/fgap/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/fgap/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index 4bcb6a0c5..3e9dc991c 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -128,7 +128,7 @@ src_install() {
#fi
doenvd "${FILESDIR}"/99fsl
- rm "${ED}"/usr/bin/cluster || die
+ mv "${ED}"/usr/bin/{,fsl_}cluster || die
}
pkg_postinst() {
diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
index 167733c42..ea03551f9 100644
--- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
+++ b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -14,7 +14,7 @@ SRC_URI="
LICENSE="GRL staden"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
IUSE=""
DEPEND="
diff --git a/sci-biology/karect/Manifest b/sci-biology/karect/Manifest
new file mode 100644
index 000000000..2360fdf9f
--- /dev/null
+++ b/sci-biology/karect/Manifest
@@ -0,0 +1 @@
+DIST karect-1.0.0.tar.gz 239445 SHA256 9d2a65af2952c994705ea196cb580511b6f28cff6722880c83cebd9fb5b25da2 SHA512 c833a862c15027eaf84eff7ddf1cf36a369fbd94bd44ab596fcee89e402e1517ba3ef2646591365d273f98f1e3f13b6ad990f73660e440f0a45c87b84a08491c WHIRLPOOL f7846ae0eae3fea4ce01c53c1203e6b290f2007bcda14117d532a475486627b15a02c5a486b80187c1b62d4faba6b9cf8a02d177c3f4c059e0d457aa220f31e3
diff --git a/sci-biology/karect/karect-1.0.0.ebuild b/sci-biology/karect/karect-1.0.0.ebuild
new file mode 100644
index 000000000..91899101e
--- /dev/null
+++ b/sci-biology/karect/karect-1.0.0.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="Correct mismatches and indels of raw reads incl. paired-end"
+HOMEPAGE="https://github.com/aminallam/karect
+ http://bioinformatics.oxfordjournals.org/content/31/21/3421.abstract"
+SRC_URI="https://codeload.github.com/aminallam/karect/legacy.tar.gz/master -> karect-1.0.0.tar.gz"
+# actually fetches aminallam-karect-v1.0-0-gba3ad54.tar.gz
+# https://github.com/aminallam/karect.git
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/aminallam-karect-ba3ad54/
+
+src_compile(){
+ $(tc-getCXX) ${CXXFLAGS} -pthread -lpthread karect.cpp -o karect || die
+}
+
+src_install(){
+ dobin karect
+ dodoc karect_manual.pdf README README.md
+}
diff --git a/sci-biology/karect/metadata.xml b/sci-biology/karect/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/karect/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
index a78d5a50a..aa8f6ca5c 100644
--- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
+++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema"
HOMEPAGE="http://manatee.sourceforge.net/igs"
@@ -36,7 +36,7 @@ DEPEND="
virtual/perl-Storable
dev-perl/Log-Log4perl
dev-perl/Log-Cabin
- dev-perl/DateManip
+ dev-perl/Date-Manip
dev-perl/IO-Tee
dev-perl/MLDBM
dev-perl/JSON
diff --git a/sci-biology/perga/metadata.xml b/sci-biology/perga/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/perga/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/perga/perga-9999.ebuild b/sci-biology/perga/perga-9999.ebuild
new file mode 100644
index 000000000..4f79d7210
--- /dev/null
+++ b/sci-biology/perga/perga-9999.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit git-r3 eutils toolchain-funcs
+
+DESCRIPTION="Paired End Reads Guided Assembler"
+HOMEPAGE="https://github.com/hitbio/PERGA
+ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252104"
+EGIT_REPO_URI="https://github.com/hitbio/PERGA.git"
+
+LICENSE="all-rights-reserved"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+ sed -e "s/gcc -g /$(tc-getCC) ${CFLAGS} ${LDFLAGS} /" -i src/Makefile || die
+ sed -e 's/-Wl,-O1//' -i src/Makefile || die
+}
+
+# does not compile with gcc-5.3.0 but 4.9.3 works
+src_compile(){
+ cd src || die
+ emake
+}
+
+src_install(){
+ dobin src/perga
+ dodoc README
+}
diff --git a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild
index cfa99d3a8..e6f00dcae 100644
--- a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild
+++ b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild
@@ -15,7 +15,7 @@ IUSE=""
DEPEND=""
RDEPEND="
- dev-perl/perl-tk
+ dev-perl/Tk
dev-perl/libwww-perl
>=sci-biology/rebase-904"
diff --git a/sci-biology/reapr/Manifest b/sci-biology/reapr/Manifest
new file mode 100644
index 000000000..bca2dc435
--- /dev/null
+++ b/sci-biology/reapr/Manifest
@@ -0,0 +1,2 @@
+DIST Reapr_1.0.18.manual.pdf 325751 SHA256 304b7b7b725abc285791d8be3b2aaf6f4afeb38852ce91fa5635dc0a9913a517 SHA512 2960d93a330bd6a0aeda749213a83dc4fcbc5128be9c6bd1917ec2abea2def9406bbedad764d48d83b7f95c2da6207a027f98b341299d85c6ed898c5ca7b370f WHIRLPOOL 39744ee90218bdcad6fc630303a9453517d7fd0ecddb357cb354ee192c32d984af0b3cb1449165ef0d81e12ef87448d4e329fd29e4264594ff15f00d2fa19482
+DIST Reapr_1.0.18.tar.gz 7966110 SHA256 6d691b5b49c58aef332e771d339e32097a7696e9c68bd8f16808b46d648b6660 SHA512 12f1e97da6b6a3d080df29d9055aaf4ab2d02eb19a6c9eecb9d1e7268bf13bbe531feda6496d4b74c63ab53db0d1be15ed72f3391c47f9b1a23c34ed6a6c5fcb WHIRLPOOL 2d8079e123785f0984f1d6c8188c7c477a6d49a8f0632e430cb4865602e5a160b8d03b5e4c9ede4653c3a88d9296261f4356ee5423d572fda7cc0218564416d6
diff --git a/sci-biology/reapr/files/fix_sort_samtools13.patch b/sci-biology/reapr/files/fix_sort_samtools13.patch
new file mode 100644
index 000000000..f009223ce
--- /dev/null
+++ b/sci-biology/reapr/files/fix_sort_samtools13.patch
@@ -0,0 +1,16 @@
+Description: adapt samtools sort usage to 1.3 syntax
+ Samtools 1.3 changed the syntax of the 'samtools sort' command, breaking
+ REAPR's smaltmap command in the process.
+ Discussed and forwarded to upstream in person, hence no URL.
+Author: Sascha Steinbiss <sascha@steinbiss.name>
+--- a/src/task_smaltmap.pl
++++ b/src/task_smaltmap.pl
+@@ -155,7 +155,7 @@
+ . " | $samtools view -S -T $assembly -b - > $raw_bam";
+
+ # sort the bam by coordinate
+-push @commands, "$samtools sort $raw_bam $raw_bam.sort";
++push @commands, "$samtools sort $raw_bam -O bam -o $raw_bam.sort.bam";
+
+ # remove duplicates
+ push @commands, "$samtools rmdup $raw_bam.sort.bam $rmdup_bam";
diff --git a/sci-biology/reapr/files/use_shared_libs.patch b/sci-biology/reapr/files/use_shared_libs.patch
new file mode 100644
index 000000000..b748c7e6d
--- /dev/null
+++ b/sci-biology/reapr/files/use_shared_libs.patch
@@ -0,0 +1,252 @@
+Description: Use_shared_libs
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,7 +1,6 @@
+-BAMTOOLS_ROOT = $(CURDIR)/bamtools
+ CC = g++
+-CFLAGS = -Wl,-rpath,$(BAMTOOLS_ROOT)/lib -Wall -O3 -I $(BAMTOOLS_ROOT)/include -L $(BAMTOOLS_ROOT)/lib
+-TABIX = tabix/tabix.o -L./tabix -ltabix -lz
++CFLAGS = -Wall -O3 -I /usr/include/bamtools -I /usr/include
++TABIX = -ltabix -lhts -lz
+ STATS_OBJS = trianglePlot.o coveragePlot.o fasta.o histogram.o utils.o
+ SCORE_OBJS = errorWindow.o utils.o histogram.o
+ BREAK_OBJS = fasta.o utils.o
+@@ -35,46 +34,46 @@
+ $(CC) $(CFLAGS) -c histogram.cpp
+
+ utils.o: utils.cpp
+- $(CC) $(CFLAGS) -lbamtools -c utils.cpp
++ $(CC) $(CFLAGS) -c utils.cpp
+
+ task_stats: task_stats.o $(STATS_OBJS)
+- $(CC) $(CFLAGS) task_stats.o $(STATS_OBJS) -lbamtools -o task_stats $(TABIX)
++ $(CC) $(CFLAGS) task_stats.o $(STATS_OBJS) -lbamtools $(TABIX) -o task_stats
+
+ task_stats.o: task_stats.cpp $(STATS_OBJS)
+ $(CC) $(CFLAGS) -c task_stats.cpp
+
+ task_score: task_score.o $(SCORE_OBJS)
+- $(CC) $(CFLAGS) task_score.o $(SCORE_OBJS) -lbamtools -o task_score $(TABIX)
++ $(CC) -o task_score $(CFLAGS) task_score.o $(SCORE_OBJS) -lbamtools $(TABIX)
+
+ task_score.o: task_score.cpp $(SCORE_OBJS)
+ $(CC) $(CFLAGS) -c task_score.cpp
+
+ task_break: task_break.o $(BREAK_OBJS)
+- $(CC) $(CFLAGS) task_break.o $(BREAK_OBJS) -lbamtools -o task_break $(TABIX)
++ $(CC) $(CFLAGS) task_break.o $(BREAK_OBJS) -lbamtools $(TABIX) -o task_break
+
+ task_break.o: task_break.cpp $(BREAK_OBJS)
+ $(CC) $(CFLAGS) -c task_break.cpp
+
+ bam2fragCov: bam2fragCov.o $(BAM2COV_OBJS)
+- $(CC) $(CFLAGS) bam2fragCov.o $(BAM2COV_OBJS) -lbamtools -o bam2fragCov $(TABIX)
++ $(CC) $(CFLAGS) bam2fragCov.o $(BAM2COV_OBJS) $(TABIX) -lbamtools -o bam2fragCov
+
+ bam2fragCov.o: bam2fragCov.cpp $(BAM2COV_OBJS)
+ $(CC) $(CFLAGS) -c bam2fragCov.cpp
+
+ bam2insert: bam2insert.o $(BAM2INSERT_OBJS)
+- $(CC) $(CFLAGS) bam2insert.o $(BAM2INSERT_OBJS) -lbamtools -o bam2insert $(TABIX)
++ $(CC) $(CFLAGS) bam2insert.o $(BAM2INSERT_OBJS) $(TABIX) -lbamtools -o bam2insert
+
+ bam2insert.o: bam2insert.cpp $(BAM2INSERT_OBJS)
+ $(CC) $(CFLAGS) -c bam2insert.cpp
+
+ bam2perfect: bam2perfect.o $(BAM2PERFECT_OBJS)
+- $(CC) $(CFLAGS) bam2perfect.o $(BAM2PERFECT_OBJS) -lbamtools -o bam2perfect $(TABIX)
++ $(CC) $(CFLAGS) bam2perfect.o $(BAM2PERFECT_OBJS) $(TABIX) -lbamtools -o bam2perfect
+
+ bam2perfect.o: bam2perfect.cpp $(BAM2PERFECT_OBJS)
+ $(CC) $(CFLAGS) -c bam2perfect.cpp
+
+ bam2fcdEstimate: bam2fcdEstimate.o $(BAM2FCDESTIMATE_OBJS)
+- $(CC) $(CFLAGS) bam2fcdEstimate.o $(BAM2FCDESTIMATE_OBJS) -lbamtools -o bam2fcdEstimate $(TABIX)
++ $(CC) $(CFLAGS) bam2fcdEstimate.o $(TABIX) $(BAM2FCDESTIMATE_OBJS) -o bam2fcdEstimate
+
+ bam2fcdEstimate.o: bam2fcdEstimate.cpp $(BAM2FCDESTIMATE_OBJS)
+ $(CC) $(CFLAGS) -c bam2fcdEstimate.cpp
+@@ -110,13 +109,13 @@
+ $(CC) $(CFLAGS) -c scaff2contig.cpp
+
+ task_gapresize: task_gapresize.o $(GAPRESIZE_OBJS)
+- $(CC) $(CFLAGS) task_gapresize.o $(GAPRESIZE_OBJS) -lbamtools -o task_gapresize $(TABIX)
++ $(CC) $(CFLAGS) task_gapresize.o $(TABIX) $(GAPRESIZE_OBJS) -o task_gapresize
+
+ task_gapresize.o: task_gapresize.cpp $(GAPRESIZE_OBJS)
+ $(CC) $(CFLAGS) -c task_gapresize.cpp
+
+ task_fcdrate: task_fcdrate.o $(FCDRATE_OBJS)
+- $(CC) $(CFLAGS) task_fcdrate.o $(FCDRATE_OBJS) -lbamtools -o task_fcdrate $(TABIX)
++ $(CC) $(CFLAGS) task_fcdrate.o $(TABIX) $(FCDRATE_OBJS) -o task_fcdrate
+
+ task_fcdrate.o: task_fcdrate.cpp $(FCDRATE_OBJS)
+ $(CC) $(CFLAGS) -c task_fcdrate.cpp
+--- a/src/task_break.cpp
++++ b/src/task_break.cpp
+@@ -10,7 +10,6 @@
+ #include <assert.h>
+ #include "fasta.h"
+ #include "utils.h"
+-#include "tabix/tabix.hpp"
+
+ using namespace std;
+
+--- a/src/task_score.cpp
++++ b/src/task_score.cpp
+@@ -18,7 +18,6 @@
+ #include "histogram.h"
+ #include "api/BamMultiReader.h"
+ #include "api/BamReader.h"
+-#include "tabix/tabix.hpp"
+
+ using namespace BamTools;
+ using namespace std;
+--- a/src/task_stats.cpp
++++ b/src/task_stats.cpp
+@@ -18,7 +18,6 @@
+ #include "utils.h"
+ #include "api/BamMultiReader.h"
+ #include "api/BamReader.h"
+-#include "tabix/tabix.hpp"
+
+ using namespace BamTools;
+ using namespace std;
+--- a/src/utils.h
++++ b/src/utils.h
+@@ -11,7 +11,7 @@
+
+ #include "api/BamMultiReader.h"
+ #include "api/BamReader.h"
+-#include "tabix/tabix.hpp"
++#include "tabix.hpp"
+
+ const short INNIE = 1;
+ const short OUTTIE = 2;
+--- a/src/task_fcdrate.cpp
++++ b/src/task_fcdrate.cpp
+@@ -9,7 +9,6 @@
+
+ #include "utils.h"
+ #include "histogram.h"
+-#include "tabix/tabix.hpp"
+
+ using namespace std;
+
+--- a/src/reapr.pl
++++ b/src/reapr.pl
+@@ -12,8 +12,8 @@
+ $this_script = File::Spec->rel2abs($this_script);
+ my ($scriptname, $scriptdir) = fileparse($this_script);
+ $scriptdir = File::Spec->rel2abs($scriptdir);
+-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
+-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
++my $tabix = 'tabix';
++my $bgzip = 'bgzip';
+ my $version = '1.0.18';
+
+ if ($#ARGV == -1) {
+--- a/src/task_preprocess.pl
++++ b/src/task_preprocess.pl
+@@ -52,9 +52,9 @@
+ my $ideal_fcd_file = File::Spec->catfile($sample_dir, 'ideal_fcd.txt');
+ my $lowess_prefix = File::Spec->catfile($sample_dir, 'gc_vs_cov.lowess');
+ my $r_script = File::Spec->catfile($sample_dir, 'gc_vs_cov.R');
+-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
+-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
+-my $samtools = File::Spec->catfile($scriptdir, 'samtools');
++my $tabix = 'tabix';
++my $bgzip = 'bgzip';
++my $samtools = 'samtools';
+
+ # make directory and soft links to required files
+ $fasta_in = File::Spec->rel2abs($fasta_in);
+--- a/src/task_perfectfrombam.pl
++++ b/src/task_perfectfrombam.pl
+@@ -57,12 +57,12 @@
+ my $min_perfect_map_qual = $ARGV[5];
+ my $min_align_score = $ARGV[6];
+ my $bam2perfect = File::Spec->catfile($scriptdir, 'bam2perfect');
+-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
+-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
++my $bgzip = 'bgzip';
++my $tabix = 'tabix';
+ my $ERROR_PREFIX = '[REAPR perfectfrombam]';
+ my $perfect_bam = "$out_prefix.tmp.perfect.bam";
+ my $repetitive_bam = "$out_prefix.tmp.repetitive.bam";
+-my $samtools = File::Spec->catfile($scriptdir, 'samtools');
++my $samtools = 'samtools';
+ my %seq_lengths;
+ my %used_seqs;
+ my $hist_file = "$out_prefix.hist";
+--- a/src/task_perfectmap.pl
++++ b/src/task_perfectmap.pl
+@@ -38,14 +38,14 @@
+ my $reads_2 = $ARGV[2];
+ my $fragsize = $ARGV[3];
+ my $preout = $ARGV[4];
+-my $findknownsnps = File::Spec->catfile($scriptdir, 'findknownsnps');
++my $findknownsnps = 'findknownsnps';
+ my $ERROR_PREFIX = '[REAPR perfect_map]';
+ my $raw_coverage_file = "$preout.tmp.cov.txt";
+ my $tmp_bin = "$preout.tmp.bin";
+ my $tmp_bin_single_match = "$tmp_bin\_single_match.fastq";
+-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
+-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
+-my $samtools = File::Spec->catfile($scriptdir, 'samtools');
++my $tabix = 'tabix';
++my $bgzip = 'bgzip';
++my $samtools = 'samtools';
+ my $all_bases_outfile = "$preout.perfect_cov.gz";
+ my $hist_outfile = "$preout.hist";
+ my @coverage = (0) x 101;
+--- a/src/task_plots.pl
++++ b/src/task_plots.pl
+@@ -50,9 +50,9 @@
+ }
+
+
+-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
+-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
+-my $samtools = File::Spec->catfile($scriptdir, 'samtools');
++my $tabix = 'tabix';
++my $bgzip = 'bgzip';
++my $samtools = 'samtools';
+ my @plot_list = ('frag_cov', 'frag_cov_cor', 'read_cov', 'read_ratio_f', 'read_ratio_r', 'clip', 'FCD_err');
+ my @file_list;
+ my $fa_out = "$outprefix.ref.fa";
+--- a/src/task_pipeline.pl
++++ b/src/task_pipeline.pl
+@@ -9,7 +9,7 @@
+
+ my ($scriptname, $scriptdir) = fileparse($0);
+ my $reapr_dir = abs_path(File::Spec->catfile($scriptdir, File::Spec->updir()));
+-my $reapr = File::Spec->catfile($reapr_dir, 'reapr');
++my $reapr = 'reapr';
+
+ my %options = (fcdcut => 0);
+
+--- a/src/task_seqrename.pl
++++ b/src/task_seqrename.pl
+@@ -7,7 +7,7 @@
+ use Getopt::Long;
+
+ my ($scriptname, $scriptdir) = fileparse($0);
+-my $samtools = File::Spec->catfile($scriptdir, 'samtools');
++my $samtools = 'samtools';
+ my %options;
+ my $usage = qq/<rename file> <in.bam> <out.bam>
+
+--- a/src/task_smaltmap.pl
++++ b/src/task_smaltmap.pl
+@@ -77,8 +77,8 @@
+ my $reads_2 = $ARGV[2];
+ my $final_bam = $ARGV[3];
+ my $ERROR_PREFIX = '[REAPR smaltmap]';
+-my $samtools = File::Spec->catfile($scriptdir, 'samtools');
+-my $smalt = File::Spec->catfile($scriptdir, 'smalt');
++my $samtools = 'samtools';
++my $smalt = 'smalt';
+ my $tmp_prefix = "$final_bam.tmp.$$.smaltmap";
+ my $smalt_index = "$tmp_prefix.smalt_index";
+ my $smalt_sample = "$tmp_prefix.smalt_sample";
diff --git a/sci-biology/reapr/metadata.xml b/sci-biology/reapr/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/reapr/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/reapr/reapr-1.0.18.ebuild b/sci-biology/reapr/reapr-1.0.18.ebuild
new file mode 100644
index 000000000..893af8b96
--- /dev/null
+++ b/sci-biology/reapr/reapr-1.0.18.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit eutils
+
+DESCRIPTION="Verify and correct genome assembly scaffolds using paired-end reads"
+HOMEPAGE="http://www.sanger.ac.uk/science/tools/reapr"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.tar.gz
+ ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_1.0.18.manual.pdf"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# tested smalt versions 0.6.4 to 0.7.0.1 only
+DEPEND="sci-biology/bamtools
+ =sci-biology/samtools-0.1.19-r2" # actually bundled is 0.1.18
+RDEPEND="${DEPEND}"
+# sci-biology/smalt
+# dev-perl/File-Basename
+# dev-perl/File-Copy
+# dev-perl/File-Spec
+# perl-core/Getopt-Long
+# dev-perl/List-Util
+# dev-lang/R"
+
+S="${WORKDIR}"/Reapr_"${PV}"
+
+# we use temporarily patches from https://anonscm.debian.org/cgit/debian-med/reapr.git/tree/debian/patches
+
+src_prepare(){
+ default
+ for f in "${FILESDIR}"/*.patch; do epatch $f || die; done
+ sed -e 's#^CC = g++#CXX ?= g++#' -i src/Makefile || die
+ sed -e 's#$(CC)#$(CXX)#' -i src/Makefile || die
+ sed -e 's#-O3##' -i src/Makefile || die
+ sed -e 's#^CFLAGS =#CXXFLAGS += -I../third_party/tabix -L../third_party/tabix -I../third_party/bamtools/src -L../third_party/bamtools/src#' -i src/Makefile || die
+ #sed -e 's#-lbamtools#../third_party/bamtools/src/libbamtools.so#' -i src/Makefile || die
+ sed -e 's#-ltabix#../third_party/tabix/libtabix.a#' -i src/Makefile || die
+ sed -e 's#CFLAGS#CXXFLAGS#' -i src/Makefile || die
+}
+
+src_compile(){
+ cd third_party/tabix || die
+ emake # to yield tabix.o object
+ cd ../.. || die
+ cd src || die
+ emake # link directly tabix.o but elsewhere also ../third_party/tabix/libtabix.a
+}
+
+src_install(){
+ dodoc "${DISTDIR}"/Reapr_"${PV}".manual.pdf
+}
+
+pkg_postinst(){
+ einfo "There are test data at ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_${PV}.test_data.tar.gz"
+ einfo "You can view results with >=sci-biology/artemis*-15.0.0"
+}
diff --git a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild b/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild
index 2c080e6b4..4b6f6450b 100644
--- a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild
+++ b/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
DESCRIPTION="Convert from ace to gap4 (of staden v1.x), not needed to convert ace for gap5 of staden v2"
HOMEPAGE="http://genome.imb-jena.de/software/roche454ace2caf"
@@ -10,7 +10,7 @@ SRC_URI="http://genome.imb-jena.de/software/roche454ace2caf/download/src/roche45
LICENSE="FLI-Jena"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
IUSE=""
DEPEND=""
diff --git a/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
index 5e57eb5dd..0a7ae5400 100644
--- a/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
+++ b/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
inherit python-r1
-DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds using a reference assembly"
+DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds using a reference genome"
HOMEPAGE="
http://sourceforge.net/projects/scaffold-b
http://edwards.sdsu.edu/scaffold_builder"
diff --git a/sci-biology/scbi_mapreduce/Manifest b/sci-biology/scbi_mapreduce/Manifest
index c1f53f0ff..78eed5135 100644
--- a/sci-biology/scbi_mapreduce/Manifest
+++ b/sci-biology/scbi_mapreduce/Manifest
@@ -1 +1 @@
-DIST scbi_mapreduce-0.0.40.gem 28160 SHA256 7898f15957da63b41fbc4d99f60821db4786c1fba12eed20dd915246acec9f70 SHA512 cdcd516b5c140308458c3050ad7e41623908d1f21d7c755d585a8ee0e38dc9f57a73e2b69090f54042f077953dc38094a0a5c5babc1f879e0a75fdacbf5accf5 WHIRLPOOL d5042b14c75962d16a9ca740bdbd589aff0e345f8a13075ac8c961564e7ef47ffbac47d114f37ec7d433383c15d19f0b02e820c0a4edd0f8c500e4c09d276e3f
+DIST scbi_mapreduce-0.0.45.gem 765440 SHA256 edb24196f9569cd1af72f89fde5ef6206f5f0fc97902975d3c842627c2266b03 SHA512 77de3fdd5f34669e8ea881c244dd69e6ecc6beab560ea4e7132f00dc77d85e6e77793f2fdf0de2d951dce05b481b71d31960b2c447f9ff91f5b250cd83833ba4 WHIRLPOOL db39c45d9a3efa1742fb3307669e39e80fecff97224fb4ed173c90856c6eaa7a1d01a3a6f6fab1b7c8aaa3e62a7b1ea8ba66008f617c38544cdc5ec11f13cfad
diff --git a/sci-biology/scbi_mapreduce/scbi_mapreduce-0.0.40.ebuild b/sci-biology/scbi_mapreduce/scbi_mapreduce-0.0.45.ebuild
index 630a7f6fb..a81de4a2d 100644
--- a/sci-biology/scbi_mapreduce/scbi_mapreduce-0.0.40.ebuild
+++ b/sci-biology/scbi_mapreduce/scbi_mapreduce-0.0.45.ebuild
@@ -6,7 +6,7 @@ EAPI=5
USE_RUBY="ruby20 ruby21"
RUBY_FAKEGEM_TASK_DOC=""
-RUBY_FAKEGEM_EXTRADOC="README.rdoc History.txt"
+RUBY_FAKEGEM_EXTRADOC="README.md"
inherit ruby-fakegem
diff --git a/sci-biology/scythe/scythe-0.992.ebuild b/sci-biology/scythe/scythe-0.992.ebuild
index 1ff2754cd..fd357912c 100644
--- a/sci-biology/scythe/scythe-0.992.ebuild
+++ b/sci-biology/scythe/scythe-0.992.ebuild
@@ -6,7 +6,7 @@ EAPI=5
inherit eutils git-r3
-DESCRIPTION="Bayesian adapter trimmer for Illumina/Solexa"
+DESCRIPTION="Bayesian 3'-end adapter (only) trimmer for Illumina/Solexa"
HOMEPAGE="https://github.com/vsbuffalo/scythe"
EGIT_REPO_URI="https://github.com/vsbuffalo/scythe"
diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest
index 8198edd23..29d8b4c6e 100644
--- a/sci-biology/staden/Manifest
+++ b/sci-biology/staden/Manifest
@@ -1,2 +1 @@
-DIST staden-2.0.0b9-src.tar.gz 4431301 SHA256 2cad8cc9821c83539e683f2bb28bbbfccbefb5bff589f71501b5cf53de8f4a8b SHA512 0818b376b9921c07cfdd36b6a62b615a3396153bbcb8714a852148457a5cc190da32af318777f07da7012e5cb45d352e8b13884176e1e85fd1707f36adff972e WHIRLPOOL 16e4070dfea1e1de30c1d7bf0e2a6c1be27c4a5364ab4e82b4bd7aea0bd4e97cfdf4e020dd418860cb79d1906bd830de94023edf1a1dc8715bdcabfb9a03141a
-DIST staden_doc-2.0.0b9-src.tar.gz 3181687 SHA256 942a560e22de0fd0da8856d2049fba1703ea042e7ea5b80e277a2d57d7fe4cd4 SHA512 9f1d1ec7f8301058574ec7da604274d1767258293c88f6cde6426ad361a8543833fa4b755e5f0109ca4dd88ea41cd7fa94f2f7e14a4d9a516ec06ae49540c15f WHIRLPOOL f5adfdd6868d565c2269b13a45ae7d19a369f61679ac918aa8e02c64667e3117fb5a4efc717d06a8bf538c75a29a24580663308ca87d4192d837c9298a5808d2
+DIST staden-2.0.0b10-src.tar.gz 4616845 SHA256 099efd84a208ec9efa3669803c0ca6f09960d760886fa3990dfa5cf9d0c112fb SHA512 6ed8316a4cd9631b1aa632dbb51c190044470898404c0cf6dadba9acd4d36f8ecc36babce00ca44d0987b9e69a457f9a333a6711d4e2cec8a9917037deda72fa WHIRLPOOL 83d896f0e7d5ee1061d8bb0463f1fbfbed6a7df650350ec825eced30883be3e3e1a447ddde2e11fd77d7044f402e015dc01df3272cae21e4538fdd0e36c3cf1f
diff --git a/sci-biology/staden/files/staden-2.0.0_beta9-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch
index 735feb315..735feb315 100644
--- a/sci-biology/staden/files/staden-2.0.0_beta9-ldflags.patch
+++ b/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch
diff --git a/sci-biology/staden/files/staden-2.0.0_beta9-zlib.patch b/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch
index 39537604e..39537604e 100644
--- a/sci-biology/staden/files/staden-2.0.0_beta9-zlib.patch
+++ b/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch
diff --git a/sci-biology/staden/files/staden-2.0.0_beta9-libpng-1.5.patch b/sci-biology/staden/files/staden-2.0.0_beta9-libpng-1.5.patch
deleted file mode 100644
index 50694a8eb..000000000
--- a/sci-biology/staden/files/staden-2.0.0_beta9-libpng-1.5.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- tk_utils/tkTrace.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tk_utils/tkTrace.c b/tk_utils/tkTrace.c
-index beeb478..42a4e11 100644
---- a/tk_utils/tkTrace.c
-+++ b/tk_utils/tkTrace.c
-@@ -2123,7 +2123,7 @@ int drawable_to_png(DNATrace *t, FILE *fp, Display *disp, Drawable d,
- goto error;
-
- /* PNG requires setjmp/longjmp to be used */
-- if (setjmp(png_ptr->jmpbuf))
-+ if (setjmp (png_jmpbuf (png_ptr)))
- goto error;
-
- /* Create the info bits */
diff --git a/sci-biology/staden/staden-2.0.0_beta9.ebuild b/sci-biology/staden/staden-2.0.0_beta10.ebuild
index 7f869140f..bc5dab7e2 100644
--- a/sci-biology/staden/staden-2.0.0_beta9.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta10.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -9,15 +9,13 @@ AUTOTOOLS_AUTORECONF=yes
inherit autotools-utils eutils flag-o-matic fortran-2 multilib
DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="http://sourceforge.net/projects/staden/"
-SRC_URI="
- http://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-src.tar.gz
- http://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"
+HOMEPAGE="http://sourceforge.net/projects/staden"
+SRC_URI="http://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-src.tar.gz"
LICENSE="staden"
SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE="curl debug fortran png tcl tk X zlib"
+KEYWORDS=""
+IUSE="debug doc fortran png tcl tk X zlib"
# either g77 or gfortran must be available
# edit src/mk/linux.mk accordingly
@@ -26,18 +24,21 @@ IUSE="curl debug fortran png tcl tk X zlib"
#
#
#
+
DEPEND="
app-arch/xz-utils
dev-lang/tk:0=
dev-tcltk/tklib
media-libs/libpng:0
- sci-biology/samtools
- >=sci-libs/io_lib-1.12.2
+ sci-biology/samtools:0
+ >=sci-libs/io_lib-1.13.8
sys-libs/zlib"
RDEPEND="${DEPEND}
>=dev-tcltk/iwidgets-4.0
tcl? ( >=dev-tcltk/itcl-3.2 )
- tk? ( >=dev-tcltk/itk-3.2 )"
+ tk? ( >=dev-tcltk/itk-3.2 )
+ net-misc/curl
+ doc? ( sci-biology/staden_doc )"
S="${WORKDIR}"/staden-${PV/_beta/b}-src
@@ -45,7 +46,6 @@ AUTOTOOLS_IN_SOURCE_BUILD=1
PATCHES=(
"${FILESDIR}"/${P}-ldflags.patch
- "${FILESDIR}"/${P}-libpng-1.5.patch
"${FILESDIR}"/${P}-zlib.patch )
src_prepare() {
@@ -69,10 +69,6 @@ src_configure(){
src_install() {
autotools-utils_src_install
- # TODO: dodoc /usr/share/doc/staden/manual/gap4.index ?
- #cd "${WORKDIR}"/staden_doc-${PV/_beta/b}-src || die "failed to cd "${WORKDIR}"/staden_doc-${PV/_beta/b}-src"
- #make install prefix="${D}"/usr || die "failed to install pre-created docs from upstream"
-
# install the LDPATH so that it appears in /etc/ld.so.conf after env-update
# subsequently, apps linked against /usr/lib/staden can be run because
# loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
@@ -81,6 +77,9 @@ src_install() {
STADENROOT="${EPREFIX}"/usr/share/staden
LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
EOF
-
doenvd "${T}"/99staden
}
+
+pkg_postinst(){
+ einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
+}
diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index ef3a75218..b785ba67c 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -16,7 +16,7 @@ ESVN_REPO_URI="https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk/sr
LICENSE="staden"
SLOT="0"
KEYWORDS=""
-IUSE="curl debug fortran png tcl tk X zlib"
+IUSE="debug doc fortran png tcl tk X zlib"
# either g77 or gfortran must be available
# edit src/mk/linux.mk accordingly
@@ -30,13 +30,15 @@ DEPEND="
dev-lang/tk:0=
dev-tcltk/tklib
media-libs/libpng:0
- sci-biology/samtools
- >=sci-libs/io_lib-1.12.2
+ sci-biology/samtools:0
+ >=sci-libs/io_lib-1.13.8
sys-libs/zlib"
RDEPEND="${DEPEND}
>=dev-tcltk/iwidgets-4.0
tcl? ( >=dev-tcltk/itcl-3.2 )
- tk? ( >=dev-tcltk/itk-3.2 )"
+ tk? ( >=dev-tcltk/itk-3.2 )
+ net-misc/curl
+ doc? ( sci-biology/staden_doc )"
AUTOTOOLS_IN_SOURCE_BUILD=1
@@ -62,13 +64,14 @@ src_configure() {
}
src_install() {
- # TODO: dodoc /usr/share/doc/staden/manual/gap4.index ?
autotools-utils_src_install SVN_VERSION="${ESVN_REVISION}"
-
cat >> "${T}"/99staden <<- EOF
STADENROOT="${EPREFIX}"/usr/share/staden
LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
EOF
-
doenvd "${T}"/99staden
}
+
+pkg_postinst(){
+ einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
+}
diff --git a/sci-biology/staden_doc/Manifest b/sci-biology/staden_doc/Manifest
new file mode 100644
index 000000000..d8f1a7c86
--- /dev/null
+++ b/sci-biology/staden_doc/Manifest
@@ -0,0 +1 @@
+DIST staden_doc-2.0.0b9-src.tar.gz 3181687 SHA256 942a560e22de0fd0da8856d2049fba1703ea042e7ea5b80e277a2d57d7fe4cd4 SHA512 9f1d1ec7f8301058574ec7da604274d1767258293c88f6cde6426ad361a8543833fa4b755e5f0109ca4dd88ea41cd7fa94f2f7e14a4d9a516ec06ae49540c15f WHIRLPOOL f5adfdd6868d565c2269b13a45ae7d19a369f61679ac918aa8e02c64667e3117fb5a4efc717d06a8bf538c75a29a24580663308ca87d4192d837c9298a5808d2
diff --git a/sci-biology/staden_doc/metadata.xml b/sci-biology/staden_doc/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/staden_doc/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/staden_doc/staden_doc-2.0.0_beta9.ebuild b/sci-biology/staden_doc/staden_doc-2.0.0_beta9.ebuild
new file mode 100644
index 000000000..df82c8d0b
--- /dev/null
+++ b/sci-biology/staden_doc/staden_doc-2.0.0_beta9.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="Documentation files for the staden package"
+HOMEPAGE="http://sourceforge.net/projects/staden"
+SRC_URI="http://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz"
+# https://sourceforge.net/p/staden/code/HEAD/tree/staden/trunk/doc/
+
+LICENSE="staden"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/perl
+ app-text/texlive
+ app-text/texi2html"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/staden_doc-${PV/_beta/b}-src
+
+# do not use texi2html-5 because it fails with:
+# texi2html -menu -verbose -split_chapter -index_chars interface.htmlinfo
+# Unknown option: index_char
+# src_prepare(){
+# # avoid running bundled texi2html code
+# sed -e "s#./tools/texi2html#texi2html#" -i manual/Makefile || die
+# }
+
+src_compile(){
+ cd manual || die
+ make -j 1 spotless || die
+ cd .. || die
+ emake -j 1 unix PAPER=A4
+}
+
+src_install(){
+ emake -j 1 install prefix="${D}"/usr
+ dodoc gkb547_gml.pdf
+}
diff --git a/sci-biology/trimmomatic/Manifest b/sci-biology/trimmomatic/Manifest
index 01342d2ba..83231f728 100644
--- a/sci-biology/trimmomatic/Manifest
+++ b/sci-biology/trimmomatic/Manifest
@@ -1,2 +1,2 @@
-DIST Trimmomatic-Src-0.32.zip 101211 SHA256 98f151f2c80b10015a74e91f22a1166c8a3d28c10c85dc59a854058ead3dd209 SHA512 d07350b826cd42feaa5a340744d93782ad8285d6d6cc2e311eaa008de54a7ee5b96198ad7caa0e285931b0add5912b4dd3d5c396887f7d0dcf33244afaec5965 WHIRLPOOL 36c897de6a30133508eb0ddfadd2dbe7012aaa817bc57039f06a0a50c93a6b25fd65189e0895d6ccb3550a6b7fc75a2a879f250843bb05d277e5eb2646ca62fc
-DIST trimmomatic-0.32_manual.pdf 338248 SHA256 bd288ff9bb15e2f27cf310d19fa0d11510fb94bf028fa254b9ab204edd1a5d20 SHA512 a306ce82f5f67c51f3ce62be9758c3c49cb6363932e1d55bb171d102b6f400a1fd3518263bf74c7ba3bac596630c6654ec7de6b055566d182eb6c9ae68e3ed38 WHIRLPOOL 0b57cad78bd46819ec5ca8389f0b7849363b34bd6c28a1563c48536b9b0537b7f7465f5e76d2ef143aafa81f8f5a7cb28626373a2178747cb50ab27583931af2
+DIST Trimmomatic-Src-0.35.zip 105326 SHA256 122bf7a9bb43f8fa499af317ed4e6e5659f16c78fac7994f88c6c9c0c9b9b153 SHA512 6bd07d57b96cb7dceb9b595bd5d228d8ca1ddb1cebb149f21a9d62a8bd6f7e474fa44fd80d0e2ec09ef0c6f1e37ec93253ad9fd9e9ed39489fce610d9825eaef WHIRLPOOL 51b4d507755b9750e57dfc8f17f88898d1a1dac6b5ef458a9d455f37225254013ba9cc1e01e95cc419cfa3de2c431246ebffc872c1e01bd5da51e2bf65224589
+DIST trimmomatic-0.35_manual.pdf 338248 SHA256 bd288ff9bb15e2f27cf310d19fa0d11510fb94bf028fa254b9ab204edd1a5d20 SHA512 a306ce82f5f67c51f3ce62be9758c3c49cb6363932e1d55bb171d102b6f400a1fd3518263bf74c7ba3bac596630c6654ec7de6b055566d182eb6c9ae68e3ed38 WHIRLPOOL 0b57cad78bd46819ec5ca8389f0b7849363b34bd6c28a1563c48536b9b0537b7f7465f5e76d2ef143aafa81f8f5a7cb28626373a2178747cb50ab27583931af2
diff --git a/sci-biology/trimmomatic/trimmomatic-0.32.ebuild b/sci-biology/trimmomatic/trimmomatic-0.35.ebuild
index 748c29335..729b90f50 100644
--- a/sci-biology/trimmomatic/trimmomatic-0.32.ebuild
+++ b/sci-biology/trimmomatic/trimmomatic-0.35.ebuild
@@ -9,7 +9,7 @@ inherit java-pkg-2 java-ant-2
DESCRIPTION="Illumina adapter trimming tool"
HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic"
SRC_URI="
- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-0.32.zip
+ http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-${PV}.zip
http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf -> "${P}"_manual.pdf"
# http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
diff --git a/sci-chemistry/nwchem/Manifest b/sci-chemistry/nwchem/Manifest
index b86a88dd1..7a6b4dc0f 100644
--- a/sci-chemistry/nwchem/Manifest
+++ b/sci-chemistry/nwchem/Manifest
@@ -1,6 +1,13 @@
DIST Bcast_ccsd.patch.gz 591 SHA256 03e0d06033a02be4f1eb659212744c822041d4619b38b48c44284bc80df4ebaf SHA512 04e08e5fee5e2b3c3d89553ad36998e180e79a59f692b1cb6848df561319c92747a307596164e86fb5b244f61df432b2b5c3170e26bc25bccdf426ba268a39d3 WHIRLPOOL 94a0dca3f6c2650362babdf465b325d2830a5dddf0a7bc74c3f31caefda142be3e1160e8499011528ac4eb4fc2e0f877dbb67ecd26ec0c490c3c5643c7763b45
+DIST Config_libs66.patch.gz 682 SHA256 aa17f03cbb22ad7d883e799e0fddad1b5957f5f30b09f14a1a2caeeb9663cc07 SHA512 50924c169e3086a419840e7593dc3126297854fac14f8e5ca9c3c47d9478bbd66d79c1e5f9f114cbe6f2a81d0197cbbf1b4085f59ac399fe076e7b96066a1946 WHIRLPOOL 142990bfa133d3356544b1814e4a11f4136804ce438f86f857c14039039ab0767df572b49cc2dd7c6b66c411b87bb938bbe704b7452b80b7214b5dedf31c4899
+DIST Cosmo_dftprint.patch.gz 424 SHA256 d3b73431a68d6733eb7b669d471e18a83e03fa8e40c48e536fe8edecd99250ff SHA512 f0930c0130bd779f7704ce8b59c1af01062ffede00102b880d1ade534fdd4867e194f5d4a9a9834f557b5708504ddceec5f3320c4ebfb5af47989261dd523920 WHIRLPOOL f4894582ab64e665dc397f03f15709d84ace4108100ef1f7cc30bb1c911142ec23b08fa4069e29341bd2af1375f16c0271d2882a1058cb575a3ab4917e9bbf20
+DIST Cosmo_meminit.patch.gz 1659 SHA256 569c5ee528f3922ee60ca831eb20ec6591633a36f80efa76cbbe41cabeb9b624 SHA512 51a7fba5a8bc3d70254bdb3d8f3ed2c538b680c3074813906cb3d068c42e7972151f9ca24ffbefc44a8b8f8478cd085feea080c6c8dae9358d62d1823b398ccd WHIRLPOOL c7311d416fb610ed87bd19ca61864786ac40ef34f47252348d5b1d6699567f349fa291ecf1e563762c1111224e3cffe519f1e139d4b90687fa250cc5ce700beb
DIST Dmapp_inc.patch.gz 234 SHA256 58e25a87d9a2844eaaae542ffa244c55c1075b040b7206771167e6458d9ca756 SHA512 ac4ea8a65316a172ec29fa8f98d03a999fae5a18aff883f20b1fb26b13867e852097d4cf5d43fa730d9ed27b81ab2ff88c92365d9429f9e67bba720603282ccc WHIRLPOOL 7a84a32c59a6a5f9a74d47686abfc75c73bc9f2e7ef8d274b9e4b90b4c9e24ca4dd46098acdb278eb7273f527e5c037557c993e263f6c4ae9999b6cdf07afd99
+DIST Dplot_tolrho.patch.gz 572 SHA256 2ebb1a5575c44eef4139da91f0e1e60057b2eccdba7f57a8fb577e840c326cbb SHA512 331754cf765e21a0236497b2a346215b7d1c985896653de70afc2e6ec8e3cec9ca2795baf3ee29d661686501eb1710944cd48966f3f5be9cf71f01d7838a1873 WHIRLPOOL c8015faa4c7543f9b1b0f02ba4792b95337ec629d993e21f6cd55906eadce9b0a3ee825aaed6f5f562becfd9e74562110c19f91fa351c5f9a337166f5c66841c
+DIST Driver_smalleig.patch.gz 255 SHA256 dd65bfbae6b472b94c8ee81d74f6c3ece37c8fc8766ff7a3551d8005d44815b8 SHA512 ae9b80e3c962404f5e41b6fd151c7b0b5758a34795be06590b5105c1ac959ee0a01c5aed9f1c6bb01765a8ecc9e5f6e24a0b80f6d80bd0612521d6dcfce4b87d WHIRLPOOL 941b1c1ad1ccdfbdbf91cc95ec140afe85963361c650bead4f60368f96eebc8ce5a52a6e9ba1e5eb2e6b89be06f88440f750c54f9c8b2b37052813af95034e5a
DIST Elpa_syncs.patch.gz 554 SHA256 ce5c45cf83d84e0a95266e667808e6e40df82e649db3b9faeb556f1e3724b8df SHA512 c6b6a11dbd40ec4ccd8e230cfd33f2667122c05572deb693ee5c516f0a7dfdefcca0bae8aef518b9cd88ce0a1aec413d3518cf29d14c0f91afdd3024ef9fd506 WHIRLPOOL 21c78a2041f5bd25475b4589c9bbef47aa98a18e7a313cea127530f21cff9f54bdecdd2b53e02e4fd991bb6f19a3399df527af2d289284070dde133aab2ca952
+DIST Ga_argv.patch.gz 244 SHA256 8a78cb2af14314b92be9d241b801e9b9fed5527b9cb47a083134c7becdfa7cf1 SHA512 63acab29c96fe2063c452d97a86bedfa9abf1b62bcb99303b13c24d40301af5f5f7427e38c8dd25e0c8225665c0412c36aa99890d5dc902e81bc65ea8b0e79e3 WHIRLPOOL bf44c14d537b050051a8c2475d2873df1c7ce7071a2b21fe82938e88121fc991485b38a9eaca49a8e1fac7de33cd82eaac8b963cb8219a822a87489283dd3812
+DIST Ga_defs.patch.gz 321 SHA256 c6f1a48338d196e1db22bcfc6087e2b2e6eea50a34d3a2b2d3e90cccf43742a9 SHA512 fb71dd6544659f8ee8d6a26efc33e335da2522759dbc380ab044ec1e827315ae1e93ad57c0cee502bb7d74584e4ca2b9d97bffcf65e3554ddc82dda42518cd44 WHIRLPOOL 9cfbdce430fc46389a0222fe6072b6670defc91011703392bab72b81f90ab0416caa8f96f1e5ef872d7d1d96754184d10475959da7384367f8c9b736181f041c
DIST Hbar.patch.gz 458 SHA256 6058010a77bc7d0bf7468dde49d7905863f2550b282abee4cceef901481272a7 SHA512 595d5250dd3d462e9d2e0b385a3b41ac828da0792e19606b0365f27b47c839e81ff16cdae590f91f48fa0ac52a4dfcee1c4929bd9054651ee27f9e7c3bf54dbc WHIRLPOOL 691ecac56d8ef8bfd377df40429e484d232b82ee28c0b546bb379d6120e00b54c408f55ccc3340e612759d1e4d72f2933f0ec40d3655ae94be03f9db3e925124
DIST Hnd_giaxyz_noinline.patch.gz 368 SHA256 4e89a383ebd0cc87b3de03133f4a0537de799e1ae938f82a6460632e324aeeb1 SHA512 a798412821e35fb3be28ff2df59ce578506635532b08f0f247bae39c85f1c0c912e5205f201f94407d9e3360e66bfb98119596bacc693165fc2b6924800c283c WHIRLPOOL f424a9773dfc45f8f6597dd5162bb10283e3b1e38b12b557089b925fa45aae02c0e988eb0785a1c7cbb5f6883df8767042e195037cc50f6a29e6cb033e5ff342
DIST Hnd_rys.patch.gz 1585 SHA256 e52eee4df9149cce039b4b1d8047d51a5f47373fe03b57c6d0f44ca23b33c06e SHA512 5e95ec72e1b1e17b324d43f3cc68003b5724295e3cad03a9ab8c58636d43ad62ab1cc42e90a5f386854bfeb02b8327ee0f6632c5bd532320e3f34080628b8d84 WHIRLPOOL 6e8eaadb3c9312e247e5c06a34848311f5921622b448c32de67e1ee2d258fcc82eff75434d8392c0fe794e6261b08736a4bea7c569a00f969575c0d87e16f7ae
@@ -8,10 +15,17 @@ DIST Ifort15_fpp_offload.patch.gz 1326 SHA256 907d86049b085bc4c2b9cb2e2554fba94e
DIST Makefile_gcc4x.patch.gz 1493 SHA256 c548c64eab196ef7aabd473379ec56c879c5a6e9e9a4d31c6503279a72094839 SHA512 35d46f78da48519ccf21b8853bfc32b958419a600ef7897135f52bc8f7dcfe733883f6600cfd88e75a8c68c3fe9fb0f6302493889df7fbc84f1dd7be29929136 WHIRLPOOL 70b7431fb11f8da971de52a4cba985548da1fa388859cf784016fc646e49d00cedf2918c9a7c47f29239b514220f47837bddff6aaa3762c5afd2c69a68bb18cb
DIST Nwchem-6.3.revision2-src.2013-10-17.tar.gz 112262489 SHA256 6a6adf068d559be1ab1bf0addc6b8aa65dbb746b8716a913f5f1bb2eb16f1718 SHA512 28b812b62bba464e6a9c76ccae17145b42ab92c460cc4372bfb6e5d48db0b618d06e778bd2f4787ffcb2d95e60e869af60739181b2f334430592764b41e5f988 WHIRLPOOL 75d4053711fcd1f69c9b3813ed00fe492aa918e75c11c60a7fb67b202bd0dfe410e80d4c7f5423ef76f4a8472db809bd91c4218159087255b495908b4be32b4b
DIST Nwchem-6.5.revision26243-src.2014-09-10.tar.gz 131069464 SHA256 9af6d7d7424809785f5a833b49d526cb3e8b5703a9e061a52e426532c48f8c75 SHA512 d4e22819bc40b3bda915dd64c68434f162ad1abccf854a480feb083858a6c8c6b9ef3347e1c5c247149347ecbb2c6dc8d4e70127b90e3b18c08d2cbf16c90843 WHIRLPOOL 9e4f7c624dc62a3e38bdac83197ca8f5d63a4625516e194211aef44f253711e1b095b5f5cbb09b3ea13448714ef2aaafd3ac1edd65f61c71dc2a3513ccc00916
+DIST Nwchem-6.6.revision27746-src.2015-10-20.tar.bz2 98351363 SHA256 7b9b324883500c412476420d3591c283c1a68068b2ab6ce185d869d82497f798 SHA512 4159cd8bcde1a703ecf221df2e0778dab4cd2239260b648d44ad7d245b8ff0b0042ec2b542892ac2b5d6a2ef86aab40f72a2db2b82d1a88a77d9872b0a42be1d WHIRLPOOL af7e6367561f071eb6585265cb8a020a6ce464f483de6b93ed63bd696beed6e1a8cc391a6b563862c8fbaef27eda0f3297ede2fd4b7f0854756a77f14d8bd6af
DIST Parallelmpi.patch.gz 216 SHA256 d30de8a7027bd5ea7672ad1fa63711a3cfc5cb118f878bc5308a142319d31420 SHA512 21d9020f77814056d3690dca71783e635a4eb951785cf12addc1ff4082b582c82399eb3c3f4f01892d5249fc30a8de1a9a18c1bf37841957bfc924d579f8f7ea WHIRLPOOL 12ac85104503ad5a14b2b67cf727ac8cd16d19311a1100e8aee612bdf1dcacc8e606b3be10c464daaf3681f22b141fd31019cfc5ed84ed5e89e33b2985c89554
DIST Print1e.patch.gz 463 SHA256 59c4d96c9da4b7fb08dee2a89afcbc6ac603c141d48cf3a16e41a92dc2a539e5 SHA512 c53105fb01bb307f7483e55adcd920a4c538cb8634af2c3fa0a13ae1899060603d67fc19392c53ae7499bef48434d667ce690ce66a50dd084bc0583fbe1d95d9 WHIRLPOOL b7562de186a0211ff97c3d378319580578fc7faa7e72ece190c852673a10101207ff779a29781559de2ac5bb373c87639c97ae4465e4a3c84e504958148d231f
+DIST Raman_displ.patch.gz 3024 SHA256 6a16f0f589a5cbb8d316f68bd2e6a0d46cd47f1c699a4b256a3973130061f6c3 SHA512 8804e2ca36a6e9724ed37bc8a3c71687ce8c560e9afeba89e6c3a51ef7818d0b5481aeb43d918dab9da9dbfb1318a86a6321980be33d2d08758f08abd1ef5e15 WHIRLPOOL ee44771d3b6430d1945337e5a38c8c97ca9ba5a0a87c5b597a3210049be537d36988c6a4773da521cd9594f53020488d342ec676157d73bff799384b53557645
+DIST Sym_abelian.patch.gz 281 SHA256 aa693e645a98dbafbb990e26145d65b100d6075254933f36326cf00bac3c29e0 SHA512 4a0728a2730ab6c7f5bfbc2ffa1f18ee83f12e287dc4a10568f10ebfadd5a6b9be281860553e5c144ae24600bb7e2549c5c8b55b5b14064e6720b14b2ab75c56 WHIRLPOOL 09d89307101c0ff7e8ac964c74e23c2fa03f5c5778a95e63999a2942713dd1a8313870fbebe4692e4fb6113ce6b9409e44709519dacb093d8fa2e5e05d2fcd14
DIST Tcenxtask.patch.gz 1556 SHA256 6b3f713024fec9a41bd7738e3cd6d31731d17a3b59a02d9a484e0a2408fcb9ca SHA512 9e11a2566c20b07a458cbd0ebe58e006b3ef04831625f3b88e38d20570945ff5138c18f148491bf890f8431699af3c180d948fe6677acf82d557c44e9a7384b5 WHIRLPOOL 8d0923a1789845be126e569a4a17703e2fda4aed9a9d2e9472d62968c9c40c38af8c40f35033bd4d644077da5ae8218c38d8ddfa82ef6313d67bfd6a5888f249
DIST Tddft_grad.patch.gz 1301 SHA256 73028f7e1d5cae1f3b1e31d30accbaec519a073696d96110ebba02cb6735ba9f SHA512 5b047f9bbd42cf5b02e651a43b65a4be95208139a75fe959267a9445fd84c8a47667d7dde24a7c02aa380a9d0d40b7dd74a4ad1051657f8bf582aa1345d45632 WHIRLPOOL 425a804dd0d3f3533a456206188a86b3ae4296508379cd6cb75938050022fd5a728a26da2c3beb20087ed7c5ebe55e8cf0eb48cdba982954806737f88aa0ec80
+DIST Tddft_mxvec20.patch.gz 55611 SHA256 cdfa8a5ae7d6ee09999407573b171beb91e37e1558a3bfb2d651982a85f0bc8f SHA512 c86299e11db3924d78c553be178ba14ccff3d2375a22b08d369908e3616ee2d890c4b4a87891a0ba7f629cd43e07e42caffa9eb1b5f06a48b3c907c91a9f9cae WHIRLPOOL 1df52d9e9d164a0eaf3692f8a14c8b5a37d1fb3e6d41a49717af6aa7d5ae1d76b01582e2e9dcfd14ed7c724b1db2fce364372e781368862a07be72ad0c1175e0
DIST Texas_iorb.patch.gz 378 SHA256 0caab84a2b9628a65232c24364c45ab29dd8637b0b29b15e1d089005eda20745 SHA512 9dc89172999606245e899a884aac073ebd40a102ba6e4164b0e548ad6cc3b37d5744b70896309c2e53871694aeb63b231b90b12e32c019ec84547b2b12e9c2f2 WHIRLPOOL 50ae525f445b4091174171fd69152a967ac48ed9ad1d0a70a9e034de27bed78ca5c7f83d9ef042ad2d19ec3b8c342cb18ee0c9d931a9d34878aa5f7779ed9702
+DIST Tools_lib64.patch.gz 286 SHA256 76b8d3e1b77829b683234c8307fde55bc9249b87410914b605a76586c8f32dae SHA512 ded09149db5074306d590dc3dfa8e8286570207bdef228831e69a4cb4189886859f10b3ebeffe99f2c8820778a864ade85f09cef624a3eddeb42b9dfa4aee260 WHIRLPOOL ba8bb0e37230150d1c8c0063e2e4bb948363339ec7ff1e86c8a4e0de7edb670c9626eb7acff030128e5e6bc739a417f338d8dc148c5b7f7411978bb30c8b37ca
DIST Util_md_sockets.patch.gz 324 SHA256 843d0d9152a3d3735557a8710ae8c6a260732a2b8e0d9ed823bbd430efff44ee SHA512 743ae8d7cdbe6612a26a10ce845003abab08c1704956940bccf249d00c1d07cf169cfb3cf648c209d5c1dc564abfeddeb8d216259f463c0d564f617c099f5e82 WHIRLPOOL cedf1d8253fb085bb6851effe25e230965cc6690441c865344f10d01e2966687753375fa3e69475378ec495c3ba85d4539417e07f2e61597060730e9f63b8f0d
+DIST Xccvs98.patch.gz 669 SHA256 1c0b0f1293e3b9b05e9e51e7d5b99977ccf1edb4b072872c8316452f6cea6f13 SHA512 e14c85ee22bf696d9e8e9f090c9c8b30b23659da28dafd020eeb18be8ab44ec66a6d4550295505b43e3428f0771e47b8c61c3ad60a0b3778b3b4e87280065d60 WHIRLPOOL 3bd212b751c4dc47165ce51ae593a69b891df74b0f60739e723945244820ac089e69e9fb106e4be44869ce53d727622365e245a4c9d88e162acafee7cee14fcb
DIST Xlmpoles_ifort15.patch.gz 256 SHA256 ae957064165afe8abcfeb580146b59b8ca680a7a5f528402047b3f8672c1e131 SHA512 f770263a22d5f680c92d52a521ddbd748633dcdf125fe75f353d70d4557fe4c8f0c25ad07e05d8452124f78523552bb87446bff10532cfccc5bc2ce941aac855 WHIRLPOOL f97940620e05d8439119e78c2ba46ea5ebae33c16b69e6bb334cf19156573a21cf0a2c8271bc76ebf3c3e27b9b0d43239d5884fccac004b7ce4a80ac5a6f5e42
+DIST Zgesvd.patch.gz 714 SHA256 4af592c047dc3e0bc4962376ae2c6ca868eb7a0b40a347ed9b88e887016ad9ed SHA512 4d057169c23fe7d109f92d1c63412c0d640f4a275c10467bce609488e54c70977af83af5afbfc4971d083ac0128652153c7af4728bb98cb3aa2b63a28c9f2cff WHIRLPOOL d994996b55835408bab306ca5a5ab7c90590d55c9c5efc649079a65ab56df6ea6ab1ea869f6a0cfe3557c4cf0b418ebbfe14f6381cb48123e1754a6959240750
diff --git a/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch b/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch
new file mode 100644
index 000000000..e129406e1
--- /dev/null
+++ b/sci-chemistry/nwchem/files/nwchem-6.6-unique_tags.patch
@@ -0,0 +1,12 @@
+diff -Naurp nwchem-6.6.orig/src/util/nwc_const.fh nwchem-6.6/src/util/nwc_const.fh
+--- nwchem-6.6.orig/src/util/nwc_const.fh 2015-10-01 17:33:14.000000000 +0000
++++ nwchem-6.6/src/util/nwc_const.fh 2015-11-26 10:53:46.386110924 +0000
+@@ -62,7 +62,7 @@
+ * Maximum number of unique tags
+ *
+ integer nw_max_unq_tags
+- parameter (nw_max_unq_tags = 40)
++ parameter (nw_max_unq_tags = nw_max_atom)
+ *------------------------------------------------------------------------------
+ * Maximum number of general contractions in a shell
+ *
diff --git a/sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild b/sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild
index 4765e8400..bf6cd69b4 100644
--- a/sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild
+++ b/sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild
@@ -193,8 +193,8 @@ src_compile() {
lapackpkg="lapack-int64"
fi
use blas && export BLASOPT="$($(tc-getPKG_CONFIG) --libs ${blaspkg})"
- use lapack && export BLASOPT+="$($(tc-getPKG_CONFIG) --libs ${lapackpkg})"
- use scalapack && export BLASOPT+="$($(tc-getPKG_CONFIG) --libs scalapack)"
+ use lapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs ${lapackpkg})"
+ use scalapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs scalapack)"
if use cuda; then
export TCE_CUDA=Y
export CUDA_PATH=/opt/cuda
diff --git a/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild b/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild
new file mode 100644
index 000000000..4c10fe832
--- /dev/null
+++ b/sci-chemistry/nwchem/nwchem-6.6_p27746-r2.ebuild
@@ -0,0 +1,279 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
+
+DATE="2015-10-20"
+
+DESCRIPTION="Delivering High-Performance Computational Chemistry to Science"
+HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page"
+PATCH_REPO="http://www.nwchem-sw.org/images"
+PATCH_LIST="Tddft_mxvec20 Tools_lib64 Config_libs66 Cosmo_meminit Sym_abelian
+Xccvs98 Dplot_tolrho Driver_smalleig Ga_argv Raman_displ Ga_defs Zgesvd Cosmo_dftprint"
+SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}.tar.bz2
+ $(for p in ${PATCH_LIST[@]}; do echo ${PATCH_REPO}/${p}.patch.gz; done)"
+
+LICENSE="ECL-2.0"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="blas cuda doc examples infiniband int64 lapack mrcc nwchem-tests openmp python scalapack"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )
+ scalapack? ( !int64 )
+ lapack? ( blas )
+ scalapack? ( blas )"
+
+RDEPEND="
+ sys-fs/sysfsutils
+ blas? ( virtual/blas )
+ lapack? ( virtual/lapack )
+ scalapack? ( virtual/scalapack )
+ cuda? ( dev-util/nvidia-cuda-sdk )
+ int64? (
+ blas? ( virtual/blas[int64] )
+ lapack? ( virtual/lapack[int64] )
+ )
+ python? ( ${PYTHON_DEPS} )"
+DEPEND="${RDEPEND}
+ virtual/pkgconfig
+ app-shells/tcsh
+ virtual/mpi[fortran]
+ infiniband? ( || (
+ sys-cluster/openmpi[fortran,openmpi_fabrics_ofed]
+ sys-cluster/mvapich2[fortran]
+ ) )
+ doc? (
+ dev-texlive/texlive-latex
+ dev-tex/latex2html )"
+
+LONG_S="${WORKDIR}/Nwchem-${PV%_p*}.revision${PV#*_p}-src.${DATE}"
+S="${WORKDIR}/${PN}-${PV%_p*}"
+
+pkg_setup() {
+ # fortran-2.eclass does not handle mpi wrappers
+ export FC="mpif90"
+ export F77="mpif77"
+ export CC="mpicc"
+ export CXX="mpic++"
+
+ use openmp && FORTRAN_NEED_OPENMP=1
+
+ fortran-2_pkg_setup
+
+ if use openmp; then
+ # based on _fortran-has-openmp() of fortran-2.eclass
+ local openmp=""
+ local fcode=ebuild-openmp-flags.f
+ local _fc=$(tc-getFC)
+
+ pushd "${T}"
+ cat <<- EOF > "${fcode}"
+ 1 call omp_get_num_threads
+ 2 end
+ EOF
+
+ for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
+ "${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break
+ done
+
+ rm -f "${fcode}.*"
+ popd
+
+ export FC="${FC} ${openmp}"
+ export F77="${F77} ${openmp}"
+ export CC="${CC} ${openmp}"
+ export CXX="${CXX} ${openmp}"
+ fi
+
+ use python && python-single-r1_pkg_setup
+}
+
+src_unpack() {
+ unpack ${A}
+ mv "${LONG_S}" "${S}"
+}
+
+src_prepare() {
+ for p in ${PATCH_LIST[@]}
+ do epatch "${WORKDIR}"/"${p}.patch"
+ done
+ epatch "${FILESDIR}"/nwchem-6.1.1-nwchemrc.patch
+ epatch "${FILESDIR}"/nwchem-6.5-icosahedron_zcoord.patch
+ epatch "${FILESDIR}"/nwchem-6.6-unique_tags.patch
+ use python && epatch "${FILESDIR}"/nwchem-6.5-python_makefile.patch
+ use doc && epatch "${FILESDIR}"/nwchem-6.3-r1-html_doc.patch
+
+ sed \
+ -e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
+ -i src/basis/MakeFile src/basis/GNUmakefile || die
+ sed \
+ -e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \
+ -i src/nwpw/libraryps/GNUmakefile || die
+ sed \
+ -e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \
+ -i src/GNUmakefile src/MakeFile || die
+
+ if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then
+ sed \
+ -e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \
+ -e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \
+ -i src/config/makefile.h || die
+ fi
+}
+
+src_compile() {
+ export NWCHEM_LONG_PATHS=Y
+ use openmp && export USE_OPENMP=1
+ export USE_MPI=y
+ export USE_MPIF=y
+ export USE_MPIF4=y
+ export MPI_LOC="${EPREFIX}"/usr
+ export MPI_INCLUDE=$MPI_LOC/include
+ export MPI_LIB=$MPI_LOC/$(get_libdir)
+ export LIBMPI="$(mpif90 -showme:link)"
+ if use infiniband; then
+ export ARMCI_NETWORK=OPENIB
+ export MSG_COMMS=MPI
+ export IB_INCLUDE="-I${MPI_INCLUDE}"
+ export IB_LIB="-L${MPI_LIB}"
+ else
+ unset ARMCI_NETWORK
+ fi
+ if [ "$ARCH" = "amd64" ]; then
+ export NWCHEM_TARGET=LINUX64
+ elif [ "$ARCH" = "ia64" ]; then
+ export NWCHEM_TARGET=LINUX64
+ elif [ "$ARCH" = "x86" ]; then
+ export NWCHEM_TARGET=LINUX
+ elif [ "$ARCH" = "ppc" ]; then
+ export NWCHEM_TARGET=LINUX
+ else
+ die "Unknown architecture"
+ fi
+ if use python ; then
+ if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then
+ export USE_PYTHON64=yes
+ fi
+ export PYTHONHOME=/usr
+ export PYTHONVERSION=$(eselect python show --python2 |awk -Fpython '{ print $2 }')
+ export PYTHONPATH="./:${S}/contrib/python/"
+ export NWCHEM_MODULES="all python"
+ else
+ export NWCHEM_MODULES="all"
+ fi
+ use mrcc && export MRCC_METHODS="TRUE" # Multi Reference Coupled Clusters
+ export CCSDTQ="TRUE" # Coupled Clusters Singlets + Dublets + Triplets + Quadruplets
+ export CCSDTLR="TRUE" # CCSDT (and CCSDTQ?) Linear Response
+ export EACCSD="TRUE" # Electron Affinities at the CCSD level
+ export IPCCSD="TRUE" # Ionisation Potentials at the CCSD level
+ unset BLASOPT
+ local blaspkg="blas"
+ local lapackpkg="lapack"
+ if use int64; then
+ blaspkg="blas-int64"
+ lapackpkg="lapack-int64"
+ fi
+ use blas && export BLASOPT="$($(tc-getPKG_CONFIG) --libs ${blaspkg})"
+ use lapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs ${lapackpkg})"
+ use scalapack && export BLASOPT+=" $($(tc-getPKG_CONFIG) --libs scalapack)"
+ if use cuda; then
+ export TCE_CUDA=Y
+ export CUDA_PATH=/opt/cuda
+ export CUDA=${CUDA_PATH}/bin/nvcc
+ export CUDA_FLAGS="-arch=compute_20 -code=sm_20,compute_20"
+ export CUDA_INCLUDE="-I${CUDA_PATH}/include"
+ export CUDA_LIBS="-L${CUDA_PATH}/$(get_libdir) -lcublas -lcufft -lcudart -lcuda -lstdc++"
+ fi
+ export LARGE_FILES="TRUE"
+
+ cd src
+ if use blas && [ "$NWCHEM_TARGET" = "LINUX64" ]; then
+ if use int64; then
+ export BLAS_SIZE=8
+ export LAPACK_SIZE=8
+ export SCALAPACK_SIZE=8
+ else
+ emake \
+ DIAG=PAR \
+ FC="$(tc-getFC)" \
+ CC="$(tc-getCC)" \
+ CXX="$(tc-getCXX)" \
+ NWCHEM_TOP="${S}" \
+ clean
+ emake \
+ DIAG=PAR \
+ FC="$(tc-getFC)" \
+ CC="$(tc-getCC)" \
+ CXX="$(tc-getCXX)" \
+ NWCHEM_TOP="${S}" \
+ 64_to_32
+ export BLAS_SIZE=4
+ export LAPACK_SIZE=4
+ export SCALAPACK_SIZE=4
+ export USE_64TO32=y
+ fi
+ fi
+ emake \
+ DIAG=PAR \
+ FC="$(tc-getFC)" \
+ CC="$(tc-getCC)" \
+ CXX="$(tc-getCXX)" \
+ NWCHEM_TOP="${S}" \
+ NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem" \
+ nwchem_config
+ emake \
+ DIAG=PAR \
+ FC="$(tc-getFC)" \
+ CC="$(tc-getCC)" \
+ CXX="$(tc-getCXX)" \
+ NWCHEM_TOP="${S}" \
+ NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem"
+
+ if use doc; then
+ cd "${S}"/doc
+ export VARTEXFONTS="${T}/fonts"
+ emake \
+ DIAG=PAR \
+ NWCHEM_TOP="${S}" \
+ pdf html
+ fi
+}
+
+src_install() {
+ dobin bin/${NWCHEM_TARGET}/nwchem
+
+ insinto /usr/share/NWChem/basis/
+ doins -r src/basis/libraries src/data
+ insinto /usr/share/NWChem/nwpw
+ doins -r src/nwpw/libraryps
+
+ insinto /etc
+ doins nwchemrc
+
+ use examples && \
+ insinto /usr/share/NWChem/ && \
+ doins -r examples
+
+ use nwchem-tests && \
+ insinto /usr/share/NWChem && \
+ doins -r QA/tests
+
+ use doc && \
+ insinto /usr/share/doc/"${P}" && \
+ doins -r doc/nwahtml && \
+ doins -r web
+
+}
+
+pkg_postinst() {
+ echo
+ elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc"
+ elog "or copy it in order to tell NWChem the right position of the"
+ elog "basis library and other necessary data."
+ echo
+}
diff --git a/sci-libs/armadillo/Manifest b/sci-libs/armadillo/Manifest
index d38dad4d3..a150ed918 100644
--- a/sci-libs/armadillo/Manifest
+++ b/sci-libs/armadillo/Manifest
@@ -1,3 +1,4 @@
DIST armadillo-4.650.4.tar.gz 5408567 SHA256 ccc56580ec932ec9beade5679b07ecbed889e9b602866f673d1a05a7692b4bf8 SHA512 a548150ba5484fce35b0bc6023982939946f2f00b733dff2cd5b46101b1c344342061389cb4363cdaa04c5e3cca3278a40febe2ed705316552dd71f841c46037 WHIRLPOOL 331493d8b9c92b9e1908880c6f6510edb12e93193a9ceb77d0b8ce9d0bfb493dc48e590ea949d39c3c19f6fc3b05446b7e00525512e3055be0f907427c28f7d4
DIST armadillo-5.600.2.tar.gz 5447327 SHA256 3a4e16f07dddd16313128eb1cab8e2f257d7461bde4a1d277c85181dcd6d1eda SHA512 68801cfcdb0cd9121a61da8d22f85f4fd781238e82b0304e7954a510e42be3da94a534b55640f912fca60c07c38828c3bab6aa4fb0328f73118ac18cd135e030 WHIRLPOOL 0e7dfff990526596fe05efe5280da0b7b60f3f2eecf98f81033b71ebaeb82fb7f243819ce7797ddcdf3290a7a810009caacaf69a1a31380bf2f013379a71917e
-DIST armadillo-6.200.3.tar.gz 5442342 SHA256 4e436704a3b0824be6286ffa7c71c91ef783699889fa0992897d446b7ed82b28 SHA512 598ba8be19971fc0e44703b17be922568e697c592ed85d0148c31f8476ecd7b5a0e6185918763bc063ba68244330b17594333c1453e9c1cfd39b9fefe85be222 WHIRLPOOL b774fd736a55c6bad44f26ed839ef7539784be494e9379b2c9fd7ff47363cfe304c23baedd24fa0c990fb94f73ce10db77a32dab77b2d6cc549e61ec83a6e33e
+DIST armadillo-6.200.5.tar.gz 5442061 SHA256 842f798be4ea2b24a8f429987d25e5b0e614e3be5a4213d76e85b7ec74faa283 SHA512 910f3a6a689fb6eee3dab16723f7d64190462e0838095fd43cc550a6bd2ae474405c4dd7571e791fb0c3ed77581163ae0cb8b1af814e125c8d298c48ffefcb21 WHIRLPOOL a517e8002b72f27902886a3aa6a0f87b70ddc99adf3f02c57b0933d1b04e19c71b03b5b8740c47a2473082252908e23acb4f5d021fee42b831ddcf0ad4a65e0c
+DIST armadillo-6.600.5.tar.gz 5461091 SHA256 6da5b32f5f2551815948bcfa5182b77b605607660d911b8f9f098f03e3cf7707 SHA512 61a7b916afaf4afcac944b05bb3dfad504fc410e2473034ef0290440df507e17744def7fb28b9917bbc2691a3749ee992201481124b62fcda2989c399ca1cb21 WHIRLPOOL d673563f0efc2c3071d1ce976d6f78994ed07af7ff1254d5258e94101b9f8dbaef28974643fb437aefecf414919be9c1d2ba8c0ed79dfb7ea242015315f5bb10
diff --git a/sci-libs/armadillo/armadillo-6.200.3.ebuild b/sci-libs/armadillo/armadillo-6.200.5.ebuild
index aba1f7b75..aba1f7b75 100644
--- a/sci-libs/armadillo/armadillo-6.200.3.ebuild
+++ b/sci-libs/armadillo/armadillo-6.200.5.ebuild
diff --git a/sci-libs/armadillo/armadillo-6.600.5.ebuild b/sci-libs/armadillo/armadillo-6.600.5.ebuild
new file mode 100644
index 000000000..aba1f7b75
--- /dev/null
+++ b/sci-libs/armadillo/armadillo-6.600.5.ebuild
@@ -0,0 +1,121 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+CMAKE_IN_SOURCE_BUILD=1
+
+inherit cmake-utils toolchain-funcs multilib eutils
+
+DESCRIPTION="Streamlined C++ linear algebra library"
+HOMEPAGE="http://arma.sourceforge.net/"
+SRC_URI="mirror://sourceforge/arma/${P}.tar.gz"
+
+LICENSE="MPL-2.0"
+SLOT="0/6"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="arpack atlas blas debug doc examples hdf5 lapack mkl superlu tbb test"
+REQUIRED_USE="test? ( lapack )"
+
+RDEPEND="
+ dev-libs/boost
+ arpack? ( sci-libs/arpack )
+ atlas? ( sci-libs/atlas[lapack] )
+ blas? ( virtual/blas )
+ lapack? ( virtual/lapack )
+ superlu? ( sci-libs/superlu )
+"
+DEPEND="${RDEPEND}
+ arpack? ( virtual/pkgconfig )
+ atlas? ( virtual/pkgconfig )
+ blas? ( virtual/pkgconfig )
+ hdf5? ( sci-libs/hdf5 )
+ lapack? ( virtual/pkgconfig )
+ mkl? ( sci-libs/mkl )
+ tbb? ( dev-cpp/tbb )"
+PDEPEND="${RDEPEND}
+ hdf5? ( sci-libs/hdf5 )
+ mkl? ( sci-libs/mkl )
+ tbb? ( dev-cpp/tbb )"
+
+src_prepare() {
+ # avoid the automagic cmake macros
+ sed -i -e '/ARMA_Find/d' CMakeLists.txt || die
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)"
+ $(cmake-utils_use debug ARMA_EXTRA_DEBUG)
+ $(cmake-utils_use mkl ARMA_USE_MKL_ALLOC)
+ $(cmake-utils_use tbb ARMA_USE_TBB_ALLOC)
+ )
+ if use arpack; then
+ mycmakeargs+=(
+ -DARPACK_FOUND=ON
+ -DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)"
+ )
+ fi
+ if use atlas; then
+ local c=atlas-cblas l=atlas-clapack
+ $(tc-getPKG_CONFIG) --exists ${c}-threads && c+=-threads
+ $(tc-getPKG_CONFIG) --exists ${l}-threads && l+=-threads
+ mycmakeargs+=(
+ -DCBLAS_FOUND=ON
+ -DCBLAS_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${c} | sed 's/-I//')"
+ -DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${c})"
+ -DCLAPACK_FOUND=ON
+ -DCLAPACK_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${l} | sed 's/-I//')"
+ -DCLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${l})"
+ )
+ fi
+ if use blas; then
+ mycmakeargs+=(
+ -DBLAS_FOUND=ON
+ -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
+ )
+ fi
+ if use hdf5; then
+ mycmakeargs+=(
+ -DHDF5_FOUND=ON
+ -DHDF5_LIBRARIES="-lhdf5"
+ )
+ fi
+ if use lapack; then
+ mycmakeargs+=(
+ -DLAPACK_FOUND=ON
+ -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
+ )
+ fi
+ if use superlu; then
+ mycmakeargs+=(
+ -DSuperLU_FOUND=ON
+ -DSuperLU_LIBRARIES="$($(tc-getPKG_CONFIG) --libs superlu)"
+ )
+ fi
+
+ cmake-utils_src_configure
+}
+
+src_test() {
+ pushd examples > /dev/null
+ emake \
+ CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \
+ EXTRA_LIB_FLAGS="-L.. $($(tc-getPKG_CONFIG) --libs blas lapack)"
+ LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die
+ LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example2 || die
+ emake clean
+ popd > /dev/null
+}
+
+src_install() {
+ cmake-utils_src_install
+ dodoc README.txt
+ use doc && dodoc *pdf && dohtml *html
+ if use examples; then
+ insinto /usr/share/examples/${PF}
+ doins -r examples/*
+ fi
+}
diff --git a/sci-libs/calculix-ccx/Manifest b/sci-libs/calculix-ccx/Manifest
index 2876cf2b3..2ac382c59 100644
--- a/sci-libs/calculix-ccx/Manifest
+++ b/sci-libs/calculix-ccx/Manifest
@@ -1,3 +1,3 @@
-DIST ccx_2.8p2.ps.tar.bz2 2404566 SHA256 8dda526c5b7911446ecadb3ded32e3d2b3daa7f232bfc88a2ad69d807acacc61 SHA512 abfe8d76e2c4fa55dea43c9a819e84dd4f8511bdb1f97c2862eb8faaa5bf314f88efabf1d8507db45d10e698cf0da0e546e108919bf4e82099f817237c1f08de WHIRLPOOL 635d5def9ae884bd2407c062afb727ab0235b64e844f6d5c302bea2fcd8e6798b930bba68c855b77ea4b4276c151bb0588e4132cd583d097908ceffa49ade4c4
-DIST ccx_2.8p2.src.tar.bz2 919489 SHA256 a21feb1a498b5925ddc9f7f58cb486d930435db4a47d5c583dd73f5160431eb2 SHA512 0ec53027ec7b072da33432b903048c5932cc51d43f5156a1ae64daf08924ed68f6bc70ea4b7fa4db9ad750bccd64c347fc7aec24418c67acaaf75c05a5988ab3 WHIRLPOOL 80587ca75690e7252303950e68b4071f14ce224d32297870589841ea1cbc7a3ad1ca257e87d84ef5ad47d688623b8cf950f2f508f4b8b9b235c9493657ada5a7
-DIST ccx_2.8p2.test.tar.bz2 9014544 SHA256 a859389cb1405a6130e06215715d4aac93b7877825d7d30a78ef3ab1f3df3662 SHA512 3d96041307b36fe342bf8ca63b041357ba818c0f72ff6217d07e0e72613aec1322a797ff2c03ecdf9cbd853f0bb79fb2e32868dc4a8ed2f20dc936a9142f9c2f WHIRLPOOL 7c859d25b3f8a9595b65bc6bb5a5f5fd8c7cd4fd0857a29b114cc0bcafc17aaf3c0c487a81ff4521ec70b2e076c4119e4913649507ea6db7900cfcf6fc79f052
+DIST ccx_2.10.ps.tar.bz2 2421249 SHA256 e7f5278b8a6efd92ca97b022afb1964792e9256b42ef9b26eb966d496a60db43 SHA512 9578d358255331045dfb3d5eccb6281f3cbaf7fdb4d0cef5cd0c19d622cba857216c7d5cba95146a1396b940a0131508509c830200c82e8c7e5ea558907aac43 WHIRLPOOL 4d1510f3ae5d327b5826753badef2671c959b2b43477f5c151ca528b0a88f66a21ab243ef6aebdcd973a723d6aa3dc7c2e75a637ab3a0cf30b58d183e15fed0c
+DIST ccx_2.10.src.tar.bz2 1005712 SHA256 693497d19d8dd2a5376e64e038d5c248d87f0e2df46d409a83bf976596b319f5 SHA512 bdd852a7fa5e327ed248058370bfaa5f029e4d98c9ee7d0e0a12f2bca480e5fc402a228e23c45f94149b2de427ebff32805f9c2a4ddbb223ff6333c26076743b WHIRLPOOL 56fb794fc8250e96ca53300ee7b4f10d7703a11a0a5e51dfe1504e320e39516e146050775a5c373180c77fdec0b090c65225e5dbac12f4a6ce5066bcbf4402e9
+DIST ccx_2.10.test.tar.bz2 9083192 SHA256 a5e00abc7f9b2a5a5f1a4f7b414617dc65cd0be9b2a66c93e20b5a25c1392a75 SHA512 9dac892b5d3d2070cc266ceeceec2aba205a81db6bb3b688a803f7768d0223c10c545cbd617628ed3ca39b13d154834eab3529a43f360991ad41d6a7771446f2 WHIRLPOOL 757fcadbb6356d9a904973ff0e6fb5644d2ec0c36ac15a0f058d310eb43c2cb91f0c34d7bfd62e0da2d8c44a4cf6ea963975e5a247a173cf80afdad78ba326b7
diff --git a/sci-libs/calculix-ccx/calculix-ccx-2.8_p2.ebuild b/sci-libs/calculix-ccx/calculix-ccx-2.10.ebuild
index f643dc931..c9eb261f8 100644
--- a/sci-libs/calculix-ccx/calculix-ccx-2.8_p2.ebuild
+++ b/sci-libs/calculix-ccx/calculix-ccx-2.10.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
inherit eutils toolchain-funcs flag-o-matic fortran-2
@@ -18,7 +18,7 @@ SRC_URI="
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="arpack doc examples threads"
+IUSE="arpack doc examples openmp threads"
RDEPEND="
arpack? ( >=sci-libs/arpack-3.1.3 )
@@ -31,9 +31,9 @@ DEPEND="${RDEPEND}
S=${WORKDIR}/CalculiX/${MY_P}/src
-src_prepare (){
- epatch "${FILESDIR}/01_${MY_P}_Makefile_custom_cc_flags_spooles_arpack.patch"
-}
+PATCHES=(
+ "${FILESDIR}/01_${MY_P}_Makefile_custom_cc_flags_spooles_arpack.patch"
+)
src_configure() {
# Technically we currently only need this when arpack is not used.
@@ -44,6 +44,11 @@ src_configure() {
if use threads; then
append-cflags "-DUSE_MT"
fi
+
+ if use openmp; then
+ append-fflags "-fopenmp"
+ append-cflags "-fopenmp"
+ fi
if use arpack; then
export ARPACKLIB=$($(tc-getPKG_CONFIG) --libs arpack)
diff --git a/sci-libs/calculix-ccx/files/01_ccx_2.10_Makefile_custom_cc_flags_spooles_arpack.patch b/sci-libs/calculix-ccx/files/01_ccx_2.10_Makefile_custom_cc_flags_spooles_arpack.patch
new file mode 100644
index 000000000..83caf80f9
--- /dev/null
+++ b/sci-libs/calculix-ccx/files/01_ccx_2.10_Makefile_custom_cc_flags_spooles_arpack.patch
@@ -0,0 +1,35 @@
+Fix Makefile to make it use custom CFLAGS and system libraries.
+
+diff -uwrN ccx_2.10.ORIG/src/Makefile ccx_2.10/src/Makefile
+--- src/Makefile 2016-03-07 04:57:09.462878788 +0100
++++ ccx_2.10/src/Makefile 2016-03-07 06:05:44.150786978 +0100
+@@ -1,9 +1,6 @@
+
+-CFLAGS = -Wall -O3 -fopenmp -I ../../../SPOOLES.2.2 -DARCH="Linux" -DSPOOLES -DARPACK -DMATRIXSTORAGE
+-FFLAGS = -Wall -O3 -fopenmp
+-
+-CC=cc
+-FC=gfortran
++CFLAGS := -Wall -DARCH="Linux" -DMATRIXSTORAGE $(CFLAGS)
++FFLAGS := -Wall $(FFLAGS)
+
+ .c.o :
+ $(CC) $(CFLAGS) -c $<
+@@ -18,15 +15,10 @@
+ OCCXC = $(SCCXC:.c=.o)
+ OCCXMAIN = $(SCCXMAIN:.c=.o)
+
+-DIR=../../../SPOOLES.2.2
+-
+-LIBS = \
+- $(DIR)/spooles.a \
+- ../../../ARPACK/libarpack_INTEL.a \
+- -lpthread -lm -lc
++LIBS = $(ARPACKLIB) $(LAPACK) -lm -lc -lspooles -lpthread
+
+ ccx_2.10: $(OCCXMAIN) ccx_2.10.a $(LIBS)
+- ./date.pl; $(CC) $(CFLAGS) -c ccx_2.10.c; $(FC) -fopenmp -Wall -O3 -o $@ $(OCCXMAIN) ccx_2.10.a $(LIBS)
++ ./date.pl; $(CC) $(CFLAGS) -c ccx_2.10.c; $(FC) $(FFLAGS) -o $@ $(OCCXMAIN) ccx_2.10.a $(LIBS)
+
+ ccx_2.10.a: $(OCCXF) $(OCCXC)
+ ar vr $@ $?
diff --git a/sci-libs/calculix-ccx/files/01_ccx_2.7_Makefile_custom_cc_flags_spooles_arpack.patch b/sci-libs/calculix-ccx/files/01_ccx_2.7_Makefile_custom_cc_flags_spooles_arpack.patch
deleted file mode 100644
index b04263492..000000000
--- a/sci-libs/calculix-ccx/files/01_ccx_2.7_Makefile_custom_cc_flags_spooles_arpack.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-diff -rupN CalculiX/ccx_2.7/src/Makefile CalculiX.patched/ccx_2.7/src/Makefile
---- CalculiX/ccx_2.7/src/Makefile 2014-03-02 09:33:28.000000000 -0500
-+++ CalculiX.patched/ccx_2.7/src/Makefile 2014-09-04 16:49:28.456612880 -0400
-@@ -1,9 +1,8 @@
-+CFLAGS := -Wall -O3 -DARCH="Linux" -DMATRIXSTORAGE $(CFLAGS)
-+FFLAGS := -Wall -O3 $(FFLAGS)
-
--CFLAGS = -Wall -O3 -I ../../../SPOOLES.2.2 -DARCH="Linux" -DSPOOLES -DARPACK -DMATRIXSTORAGE
--FFLAGS = -Wall -O3
--
--CC=cc
--FC=gfortran
-+#CC:=cc
-+#FC:=gfortran
-
- .c.o :
- $(CC) $(CFLAGS) -c $<
-@@ -18,12 +17,7 @@ OCCXF = $(SCCXF:.f=.o)
- OCCXC = $(SCCXC:.c=.o)
- OCCXMAIN = $(SCCXMAIN:.c=.o)
-
--DIR=../../../SPOOLES.2.2
--
--LIBS = \
-- $(DIR)/spooles.a \
-- ../../../ARPACK/libarpack_INTEL.a \
-- -lpthread -lm -lc
-+LIBS = $(ARPACKLIB) $(LAPACK) -lm -lc -lspooles -lpthread
-
- ccx_2.7: $(OCCXMAIN) ccx_2.7.a $(LIBS)
- ./date.pl; $(CC) $(CFLAGS) -c ccx_2.7.c; $(FC) -Wall -O3 -o $@ $(OCCXMAIN) ccx_2.7.a $(LIBS)
diff --git a/sci-libs/calculix-ccx/files/01_ccx_2.7_lapack.patch b/sci-libs/calculix-ccx/files/01_ccx_2.7_lapack.patch
deleted file mode 100644
index cc83fca94..000000000
--- a/sci-libs/calculix-ccx/files/01_ccx_2.7_lapack.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-diff -rupN CalculiX/ccx_2.7/src/Makefile.inc CalculiX.patch/ccx_2.7/src/Makefile.inc
---- CalculiX/ccx_2.7/src/Makefile.inc 2014-03-02 09:33:27.000000000 -0500
-+++ CalculiX.patch/ccx_2.7/src/Makefile.inc 2014-08-30 11:18:14.914823360 -0400
-@@ -128,7 +128,6 @@ depvars.f \
- deuldlag.f \
- dflux.f \
- dfluxs.f \
--dgesv.f \
- distattach.f \
- distattach_3d.f \
- distattachline.f \
diff --git a/sci-libs/calculix-ccx/files/01_ccx_2.8p2_Makefile_custom_cc_flags_spooles_arpack.patch b/sci-libs/calculix-ccx/files/01_ccx_2.8p2_Makefile_custom_cc_flags_spooles_arpack.patch
deleted file mode 100644
index a47fdc6f1..000000000
--- a/sci-libs/calculix-ccx/files/01_ccx_2.8p2_Makefile_custom_cc_flags_spooles_arpack.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-Fix Makefile to make it use custom CFLAGS and system libraries.
-
---- CalculiX.orig/ccx_2.8p2/src/Makefile 2015-05-21 11:04:58.125111330 +0300
-+++ CalculiX/ccx_2.8p2/src/Makefile 2015-05-21 11:08:26.848130631 +0300
-@@ -1,9 +1,9 @@
-
--CFLAGS = -Wall -O3 -I ../../../SPOOLES.2.2 -DARCH="Linux" -DSPOOLES -DARPACK -DMATRIXSTORAGE
--FFLAGS = -Wall -O3 -fopenmp
-+CFLAGS := -Wall -O3 -DARCH="Linux" -DMATRIXSTORAGE $(CFLAGS)
-+FFLAGS := -Wall -O3 $(FFLAGS)
-
--CC=cc
--FC=gfortran
-+#CC=cc
-+#FC=gfortran
-
- .c.o :
- $(CC) $(CFLAGS) -c $<
-@@ -18,12 +18,7 @@
- OCCXC = $(SCCXC:.c=.o)
- OCCXMAIN = $(SCCXMAIN:.c=.o)
-
--DIR=../../../SPOOLES.2.2
--
--LIBS = \
-- $(DIR)/spooles.a \
-- ../../../ARPACK/libarpack_INTEL.a \
-- -lpthread -lm -lc
-+LIBS = $(ARPACKLIB) $(LAPACK) -lm -lc -lspooles -lpthread
-
- ccx_2.8p2: $(OCCXMAIN) ccx_2.8p2.a $(LIBS)
- ./date.pl; $(CC) $(CFLAGS) -c ccx_2.8p2.c; $(FC) -fopenmp -Wall -O3 -o $@ $(OCCXMAIN) ccx_2.8p2.a $(LIBS)
diff --git a/sci-libs/calculix-cgx/Manifest b/sci-libs/calculix-cgx/Manifest
index 4faa77e9d..b5d231084 100644
--- a/sci-libs/calculix-cgx/Manifest
+++ b/sci-libs/calculix-cgx/Manifest
@@ -1,2 +1,2 @@
-DIST cgx_2.7.all.tar.bz2 1660205 SHA256 5378a664b52e64910afb896885fe63e1a2e639f3b4e0256eef4e71e96c6a10d2 SHA512 2e0fb80d4bb2d1a8f0ce5d04e542b42d3a616702fa176eaf533959f8e968a181877c79f5bb9f88980684004a766c3eb91fb9e393511ee787efe6632308004ced WHIRLPOOL ac57eeba70a8999014650f4360699bf671b71b3d402d297653d893aad45b5bbe89f363fe07fde8bdf999324af81fa5f0a699eddf0412040a71c97f6e57d88074
-DIST cgx_2.7.pdf 1082452 SHA256 8af937b79236085e6caf5b9b399cafaebda7a9dda0193522cd00ed5a09d18363 SHA512 49ff74be3ccf68f10a240093cf9fae2bcabaeb8acfe3511926df7fe3523f0ff66a130b2fa727504ff4787589ba6ee65ced76d229c315ad7306cbc665bc055c60 WHIRLPOOL 981890f2c7ee5e00de65f8a13a2eae097689bdc5f58956a2864c525950c68683794952f92149334a2e6538dcde47ff369194c644f5371cce4b9be9f6d27fec41
+DIST cgx_2.10.all.tar.bz2 1701663 SHA256 b2ea974003374c28b8e24f76f8a6c142db470a8c2a53013e3735efe78e98e84d SHA512 ac4dce3ffee63aa7be7ee441b7ae31a3839e6322175b70449e3c72bff3ed0bf3ade66170dd47f00d6ef488729f987f622a7db9cde3e69ad7cf38b9b096c931fd WHIRLPOOL a5186a8667e6272c669ed1f5214028235ca2179eb59f08abaa09ded64875aaeae6ab2541da6fbd6494b16b489ca2f1e68185e726fc3bc5be6bf03ed1df9d1b40
+DIST cgx_2.10.pdf 1178710 SHA256 b9bc56222496283948e151e3b1e07e4295cefba20ff9a567221bfbdb2c68b654 SHA512 cedf7556e85f631aa475d25325587aea2ecad650c325762080524dd056ba1e247d677c9ae2bcb2736b9c0a402a9060dbdebff834d8c10e3d127ecc3af9106385 WHIRLPOOL a10b68ec7772a0f98aa620b70c17b6293bf6a44647ee0a293b0629f5db6488a232b2c32cb632d77550b756293e307c4dfcd52fc3f3ccb8f73ec8ef9c6c4a4aef
diff --git a/sci-libs/calculix-cgx/calculix-cgx-2.7-r1.ebuild b/sci-libs/calculix-cgx/calculix-cgx-2.10.ebuild
index d00703657..0535bb835 100644
--- a/sci-libs/calculix-cgx/calculix-cgx-2.7-r1.ebuild
+++ b/sci-libs/calculix-cgx/calculix-cgx-2.10.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
inherit eutils
@@ -20,35 +20,36 @@ KEYWORDS="~amd64 ~x86"
IUSE="doc examples"
RDEPEND="media-libs/mesa[nptl]
- >=media-libs/freeglut-1.0"
+ >=media-libs/freeglut-1.0
+ virtual/opengl
+ x11-libs/libX11
+ x11-libs/libXmu
+ x11-libs/libXi
+ x11-libs/libXext
+ x11-libs/libXt
+ x11-libs/libSM
+ x11-libs/libICE"
DEPEND="${RDEPEND}
doc? ( app-text/ghostscript-gpl )"
S=${WORKDIR}/CalculiX/${MY_P}/src/
-src_unpack() {
- default
- cp "${DISTDIR}/${MY_P}.pdf" "${S}"
-}
-src_prepare() {
- epatch "${FILESDIR}"/01_${MY_P}_Makefile_custom_cxx_flags.patch
- epatch "${FILESDIR}"/02_${MY_P}_menu_fix-freeglut_2.8.1.patch
-}
+PATCHES=(
+ "${FILESDIR}"/01_${MY_P}_Makefile_custom_cxx_flags.patch
+ "${FILESDIR}"/02_${MY_P}_menu_fix-freeglut_2.8.1.patch
+)
src_configure () {
# Does not compile without -lpthread
- #if use nptl; then
export PTHREAD="-lpthread"
- #else
- # export PTHREAD=""
- #fi
+ export LFLAGS="-L/usr/$(get_libdir) ${LFLAGS}"
}
src_install () {
dobin cgx
if use doc; then
- dodoc ${MY_P}.pdf
+ dodoc "${DISTDIR}/${MY_P}.pdf"
fi
if use examples; then
diff --git a/sci-libs/calculix-cgx/files/01_cgx_2.7_Makefile_custom_cxx_flags.patch b/sci-libs/calculix-cgx/files/01_cgx_2.10_Makefile_custom_cxx_flags.patch
index 0c97613a0..d6e22f9c9 100644
--- a/sci-libs/calculix-cgx/files/01_cgx_2.7_Makefile_custom_cxx_flags.patch
+++ b/sci-libs/calculix-cgx/files/01_cgx_2.10_Makefile_custom_cxx_flags.patch
@@ -1,30 +1,30 @@
-diff -rupN CalculiX/cgx_2.7/src/Makefile CalculiX.patched/cgx_2.7/src/Makefile
---- CalculiX/cgx_2.7/src/Makefile 2014-02-18 13:47:05.000000000 -0500
-+++ CalculiX.patched/cgx_2.7/src/Makefile 2014-09-04 17:08:58.043266103 -0400
+diff -uwrN cgx_2.10.ORIG/src/Makefile cgx_2.10/src/Makefile
+--- src/Makefile 2016-01-13 12:41:40.398930000 +0100
++++ cgx_2.10/src/Makefile 2016-03-08 11:02:59.591853482 +0100
@@ -1,15 +1,15 @@
-CFLAGS = -O3 -Wall \
-+CFLAGS := -O3 -Wall \
++CFLAGS += -Wall \
-I./ \
-I/usr/include \
-I/usr/include/GL \
-I../../libSNL/src \
-I../../glut-3.5/src \
- -I/usr/X11/include
-+ -I/usr/X11/include $(CFLAGS)
++ -I/usr/include/X11
-LFLAGS = \
- -L/usr/lib64 -lGL -lGLU \
- -L/usr/X11R6/lib64 -lX11 -lXi -lXmu -lXext -lXt -lSM -lICE \
- -lm -lpthread -lrt
-+LFLAGS := \
-+ -L/usr/lib -lGL -lGLU -lglut \
-+ -L/usr/X11R6/lib -lX11 -lXi -lXmu -lXext -lXt -lSM -lICE \
-+ -lm $(PTHREAD) -lrt $(LFLAGS)
++LFLAGS += \
++ -lGL -lGLU -lglut\
++ -lX11 -lXi -lXmu -lXext -lXt -lSM -lICE \
++ -lm $(PTHREAD) -lrt
# on 32bit systems change lib64 to lib
-@@ -19,41 +19,6 @@ LFLAGS = \
- include Makefile.inc
+@@ -22,41 +22,6 @@
+ userFunction.c
SUTIL = \
- ../../glut-3.5/src/layerutil.c \
@@ -65,12 +65,9 @@ diff -rupN CalculiX/cgx_2.7/src/Makefile CalculiX.patched/cgx_2.7/src/Makefile
uselibSNL.cpp \
generateTet.cpp \
../../libSNL/src/*.cpp
-@@ -62,7 +27,7 @@ OLIB = $(SLIB:.c=.o)
+@@ -66,7 +31,7 @@
OUTIL = $(SUTIL:.c=.o)
- cgx: $(OLIB) $(OUTIL)
-- g++ $(OLIB) $(OUTIL) $(CFLAGS) $(LFLAGS) -o $@
-+ $(CXX) $(OLIB) $(OUTIL) $(CFLAGS) $(LFLAGS) -o $@
-
-
-
+ cgx: $(OLIB) $(OUTIL) $(OULIB)
+- g++ $(OULIB) $(OLIB) $(OUTIL) $(CFLAGS) $(LFLAGS) -o $@
++ $(CXX) $(OULIB) $(OLIB) $(OUTIL) $(CFLAGS) $(LFLAGS) -o $@
diff --git a/sci-libs/calculix-cgx/files/02_cgx_2.7_menu_fix-freeglut_2.8.1.patch b/sci-libs/calculix-cgx/files/02_cgx_2.10_menu_fix-freeglut_2.8.1.patch
index 8f304afac..ff440b44e 100644
--- a/sci-libs/calculix-cgx/files/02_cgx_2.7_menu_fix-freeglut_2.8.1.patch
+++ b/sci-libs/calculix-cgx/files/02_cgx_2.10_menu_fix-freeglut_2.8.1.patch
@@ -1,7 +1,7 @@
-diff -rupN CalculiX/cgx_2.7/src/cgx.c CalculiX.patched/cgx_2.7/src/cgx.c
---- CalculiX/cgx_2.7/src/cgx.c 2014-02-18 13:43:53.000000000 -0500
-+++ CalculiX.patched/cgx_2.7/src/cgx.c 2014-09-07 10:59:21.396969109 -0400
-@@ -240,6 +240,9 @@ int subsubmenu_entity=-1, subsubmenu_p
+diff -uwrN cgx_2.10.ORIG/src/cgx.c cgx_2.10/src/cgx.c
+--- src/cgx.c 2016-03-04 20:40:43.429549000 +0100
++++ cgx_2.10/src/cgx.c 2016-03-08 10:53:56.816865592 +0100
+@@ -242,6 +242,9 @@
int subsubmenu_animTune=-1, subsubmenu_animSteps=-1;
int subsubmenu_animPeriod=-1;
@@ -11,20 +11,20 @@ diff -rupN CalculiX/cgx_2.7/src/cgx.c CalculiX.patched/cgx_2.7/src/cgx.c
GLfloat lmodel_twoside[] = { GL_TRUE };
GLfloat lmodel_oneside[] = { GL_FALSE };
double dx ,dy; /* Mauskoordinaten im bereich +-1*/
-@@ -397,6 +400,12 @@ void allocUtilityData(void)
+@@ -400,7 +403,11 @@
+ #endif
}
-
+-
+void queueRecompileEntitiesInMenu(int lc)
+{
+ recompileFlag = 1;
+ recompileMenu = lc;
+}
-+
-
- #if INX_MODE
-@@ -3105,7 +3114,7 @@ void selectDataset( int selection )
+ /* the node pointer must not be changed inside the function. Since that is the case the *node is changed to *node_dummy
+ and the global *node is used which is always correct so far */
+@@ -3201,7 +3208,7 @@
seqLC[2]=anz->l-1;
}/* no sequence until a new entity is selected and all data are prepared */
@@ -33,7 +33,7 @@ diff -rupN CalculiX/cgx_2.7/src/cgx.c CalculiX.patched/cgx_2.7/src/cgx.c
}
-@@ -3133,7 +3142,15 @@ void createNewMainMenu(void)
+@@ -3229,7 +3236,15 @@
glutSetWindow( activWindow);
}
@@ -50,7 +50,7 @@ diff -rupN CalculiX/cgx_2.7/src/cgx.c CalculiX.patched/cgx_2.7/src/cgx.c
void recompileEntitiesInMenu(int lc)
{
-@@ -5486,6 +5503,7 @@ int main ( int argc, char **argv )
+@@ -5918,6 +5933,7 @@
glutSpecialFunc ( specialKeyboard );
glutEntryFunc ( entryfunktion );
glutPassiveMotionFunc ( Mouse );
@@ -58,16 +58,15 @@ diff -rupN CalculiX/cgx_2.7/src/cgx.c CalculiX.patched/cgx_2.7/src/cgx.c
glDisable(GL_DITHER);
glLightModelfv(GL_LIGHT_MODEL_TWO_SIDE, lmodel_oneside);
glCullFace ( GL_BACK );
-diff -rupN CalculiX/cgx_2.7/src/extUtil.h CalculiX.patched/cgx_2.7/src/extUtil.h
---- CalculiX/cgx_2.7/src/extUtil.h 2014-02-18 13:44:22.000000000 -0500
-+++ CalculiX.patched/cgx_2.7/src/extUtil.h 2014-09-07 10:54:05.816962047 -0400
-@@ -34,7 +34,8 @@ void printf_fflush(const char *fmt,...);
+diff -uwrN cgx_2.10.ORIG/src/extUtil.h cgx_2.10/src/extUtil.h
+--- src/extUtil.h 2016-02-13 02:21:44.342442000 +0100
++++ cgx_2.10/src/extUtil.h 2016-03-08 10:55:36.194863375 +0100
+@@ -34,7 +34,7 @@
}
#endif
#else
- #include <GL/glut_cgx.h>
-+ //#include <GL/glut_cgx.h>
+ #include <GL/glut.h>
#endif
- #define PI 3.14159265358979323846264338327950288
+ #define PI 3.14159265358979323846264338327950288 \ No newline at end of file
diff --git a/sci-libs/clfft/Manifest b/sci-libs/clfft/Manifest
index 63bf028f2..c3f6d26d2 100644
--- a/sci-libs/clfft/Manifest
+++ b/sci-libs/clfft/Manifest
@@ -1,3 +1,4 @@
DIST clfft-2.10.0.tar.gz 986031 SHA256 f70d8ae7b8c38f27b4f28e5e7abe55378e18c4f1c5cf8922b561dc908d36ffdc SHA512 45f023bfdaf2294dc47704371dda2531aedde49977e7a9b810998a3be972fae70c44fb0ad6285e247fb6a428e00c056ab1698443d339edebdc84a37f091e528d WHIRLPOOL 70c367bb1b77e0868c3125cd4054616418f68c3ec85805d0f0059a49e3e3f5452342d1f608c6919ba052ad1ffe1505aef2775590e9ced887a95aeeb80e5bed7a
+DIST clfft-2.10.2.tar.gz 988720 SHA256 7be3a706a533e1a54f9b78e13f91d19603ce082fb32c25b48d1216f5424515d7 SHA512 4f192ddf2f578aeadc350534b28036618b15a77bd216231283597515de5cef558d8e1aead1345d8f03f76dba17e41bc001af7845f502d16effa18c093f3acffe WHIRLPOOL 94cb59852b879df74e98fb7a12bdcacac9edfdd393a5aaab405b3dfa72f5c3775169135ad84d0ca627a095fcdfb73f71c8900b0d1bc707b0ee0433a9260d5025
DIST clfft-2.6.1.tar.gz 893794 SHA256 2b5b15b903baeef4dcea6bb8efbe6aba284510148c04d20f9b151a94ae71c050 SHA512 6022ba6a2f09ae3139c3869464fb7807b0a76f26ef9b9cc856f65abc3e6278004242ebbe3d259406bc8a619684f5ccf24b2019bdbe4dfaf6c745572e0a0ae4b0 WHIRLPOOL 9a61d7c84bccf4744983a851e97cfd4d5b8cd0d7d868d8adc6a022a535b681f13d6ab687d42e5e2ca2773f560ef93403d705ee4f9caa970fa17d45ea525956dc
DIST clfft-2.8.tar.gz 967253 SHA256 9964b537f0af121560e64cb5a2513b153511ca85e011f23a332c45cc66f3d60a SHA512 73a1ee5373173c33bd25d2f28f46d7744fe35c4c8d1b38bede0efadd37f8199e547881eb62b04d33d6785fcddbd09512d934f88abad662a1e6c5c6299beae5ce WHIRLPOOL 529c242d1f2bf4030da96640a57a6a8c4d807be010cfc89546f2ebd99ae4f17c5d3281f60308ec98e662c6f28947fec4aa45708a7c0f1742e76d60a567c94822
diff --git a/sci-libs/clfft/clfft-2.10.2.ebuild b/sci-libs/clfft/clfft-2.10.2.ebuild
new file mode 100644
index 000000000..1776ddd5f
--- /dev/null
+++ b/sci-libs/clfft/clfft-2.10.2.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils
+
+MY_PN="clFFT"
+
+DESCRIPTION="Library containing FFT functions written in OpenCL"
+HOMEPAGE="https://github.com/clMathLibraries/clFFT"
+SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="callback_client +client examples test"
+
+RDEPEND="
+ >=sys-devel/gcc-4.6:*
+ virtual/opencl
+ dev-libs/boost"
+DEPEND="${RDEPEND}"
+# test? (
+# dev-cpp/gtest
+# sci-libs/fftw:3.0
+# )"
+
+# The tests only get compiled to an executable named Test, which is not recogniozed by cmake.
+# Therefore src_test() won't execute any test.
+RESTRICT="test"
+
+S="${WORKDIR}/${MY_PN}-${PV}/src"
+
+pkg_pretend() {
+ if [[ ${MERGE_TYPE} != binary ]]; then
+ if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then
+ die "Compilation with gcc older than 4.6 is not supported."
+ fi
+ fi
+}
+
+src_configure() {
+ local mycmakeargs=(
+ $(cmake-utils_use_build callback_client CALLBACK_CLIENT)
+ $(cmake-utils_use_build client CLIENT)
+ $(cmake-utils_use_build examples EXAMPLES)
+ $(cmake-utils_use_build test TEST)
+ -DBoost_USE_STATIC_LIBS=OFF
+ )
+ cmake-utils_src_configure
+}
diff --git a/sci-libs/io_lib/Manifest b/sci-libs/io_lib/Manifest
new file mode 100644
index 000000000..d4e42385d
--- /dev/null
+++ b/sci-libs/io_lib/Manifest
@@ -0,0 +1 @@
+DIST io_lib-1.14.7.tar.gz 2177248 SHA256 e75e463f62cd97bf58cf52bed76362af5e19823248be858dfeb85bdca107c754 SHA512 c1021f0a0dd284e8abbf9cc1dd11995550cf6621455c873effaab56b573fee053ed9e55879003c735c26c403a0aa34d75be87d337cd515cc912706abe7e08665 WHIRLPOOL 43a97772cfa1e9684ed0866c243fa32a6647290ba0bd40b6edf0dce01542249216a08337acca81f06f1a7b54b561ee84cf7c66872234b0b6c8b3f60595373e1d
diff --git a/sci-libs/io_lib/io_lib-1.14.7.ebuild b/sci-libs/io_lib/io_lib-1.14.7.ebuild
new file mode 100644
index 000000000..a0704a28c
--- /dev/null
+++ b/sci-libs/io_lib/io_lib-1.14.7.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools-utils
+
+DESCRIPTION="General purpose trace and experiment file reading/writing interface"
+HOMEPAGE="http://staden.sourceforge.net/"
+SRC_URI="mirror://sourceforge/staden/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="static-libs"
+
+# Prototype changes in io_lib-1.9.0 create incompatibilities with BioPerl. (Only
+# versions 1.8.11 and 1.8.12 will work with the BioPerl Staden extensions.)
+#DEPEND="!sci-biology/bioperl"
+DEPEND="
+ net-misc/curl
+ sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+src_install() {
+ autotools-utils_src_install
+ dodoc docs/{Hash_File_Format,ZTR_format}
+}
diff --git a/sci-libs/io_lib/metadata.xml b/sci-libs/io_lib/metadata.xml
new file mode 100644
index 000000000..a88279ec5
--- /dev/null
+++ b/sci-libs/io_lib/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <longdescription>
+ io_lib is a library of file reading and writing code to provide a
+ general purpose trace file (and Experiment File) reading interface. The
+ programmer simply calls the (eg) read_reading to create a "Read" C structure
+ with the data loaded into memory.
+</longdescription>
+ <upstream>
+ <remote-id type="sourceforge">staden</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sys-cluster/modules/modules-3.2.10-r1.ebuild b/sys-cluster/modules/modules-3.2.10-r1.ebuild
index 5bf51febc..7408bc869 100644
--- a/sys-cluster/modules/modules-3.2.10-r1.ebuild
+++ b/sys-cluster/modules/modules-3.2.10-r1.ebuild
@@ -57,5 +57,5 @@ src_install() {
exeinto /usr/share/Modules/bin
doexe "${FILESDIR}"/createmodule.{sh,py}
dosym /usr/share/Modules/init/csh /etc/profile.d/modules.csh
- dodir /etc/modulesfiles
+ dodir /etc/modulefiles
}