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-rw-r--r--sci-biology/AlignGraph/AlignGraph-9999.ebuild3
-rw-r--r--sci-biology/Atlas/Atlas-2005.ebuild12
-rw-r--r--sci-biology/BBmap/BBmap-36.02.ebuild43
-rw-r--r--sci-biology/BBmap/Manifest1
-rw-r--r--sci-biology/bcftools/bcftools-1.2.ebuild6
-rw-r--r--sci-biology/biopieces/biopieces-0.51.ebuild8
-rw-r--r--sci-biology/biopieces/biopieces-9999.ebuild8
-rw-r--r--sci-biology/biopieces/metadata.xml2
-rw-r--r--sci-biology/blasr/blasr-9999.ebuild18
-rw-r--r--sci-biology/grappa/grappa-2.0.ebuild3
-rw-r--r--sci-biology/jannovar-bin/Manifest2
-rw-r--r--sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild30
-rw-r--r--sci-biology/jannovar-bin/metadata.xml12
-rw-r--r--sci-biology/jannovar/Manifest1
-rw-r--r--sci-biology/jannovar/jannovar-0.16.ebuild36
-rw-r--r--sci-biology/jannovar/metadata.xml12
-rw-r--r--sci-biology/prokka/prokka-1.11.ebuild2
17 files changed, 177 insertions, 22 deletions
diff --git a/sci-biology/AlignGraph/AlignGraph-9999.ebuild b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
index 9754ee5f0..f6ea6bb6d 100644
--- a/sci-biology/AlignGraph/AlignGraph-9999.ebuild
+++ b/sci-biology/AlignGraph/AlignGraph-9999.ebuild
@@ -10,7 +10,7 @@ if [ "$PV" == "9999" ]; then
inherit git-r3
fi
-DESCRIPTION="Reference-assisted asssembly of contigs/scaffolds"
+DESCRIPTION="Reference-genome-assisted asssembly of contigs/scaffolds using PE reads"
HOMEPAGE="https://github.com/baoe/AlignGraph
http://bioinformatics.oxfordjournals.org/content/30/12/i319.long"
if [ "$PV" == "9999" ]; then
@@ -27,6 +27,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
+ sci-biology/mummer
sci-biology/blat
sci-biology/bowtie"
diff --git a/sci-biology/Atlas/Atlas-2005.ebuild b/sci-biology/Atlas/Atlas-2005.ebuild
index c66660bdb..c95df06c2 100644
--- a/sci-biology/Atlas/Atlas-2005.ebuild
+++ b/sci-biology/Atlas/Atlas-2005.ebuild
@@ -14,5 +14,15 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND=""
+DEPEND="dev-libs/boost"
RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/atlas-src
+
+src_compile(){
+ # install headers, bins and libs into CBT_DEVEL_USER, then compile apps
+ cd src || die
+ emake CBT_DEVEL_DIR="${S}"/CBT CBT_INSTALL_DIR="${D}"
+ cd ../CBTApps || die
+ emake CBT_DEVEL_DIR="${S}"/CBT CBT_INSTALL_DIR="${D}"
+}
diff --git a/sci-biology/BBmap/BBmap-36.02.ebuild b/sci-biology/BBmap/BBmap-36.02.ebuild
new file mode 100644
index 000000000..fa463a306
--- /dev/null
+++ b/sci-biology/BBmap/BBmap-36.02.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool"
+HOMEPAGE="http://sourceforge.net/projects/bbmap/"
+SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="
+ sys-cluster/openmpi[java]
+ >=virtual/jdk-1.7:*
+ dev-java/ant-core"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.7:*"
+
+S="${WORKDIR}"/bbmap
+
+src_prepare(){
+ # fix the line in build.xml to point to mpi.jar location
+ # <property name="mpijar" location="/tmp/mpi.jar" ></property>
+ # see bug #542700
+ sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml
+ sed -e 's#compiler="${jcompiler}" ##' -i build.xml
+}
+
+src_compile(){
+ ant dist || die
+}
+
+src_install(){
+ dobin *.sh
+ dodoc docs/readme.txt
+ java-pkg_dojar dist/lib/BBTools.jar
+}
diff --git a/sci-biology/BBmap/Manifest b/sci-biology/BBmap/Manifest
index de0622d2a..c9c39e012 100644
--- a/sci-biology/BBmap/Manifest
+++ b/sci-biology/BBmap/Manifest
@@ -1,2 +1,3 @@
DIST BBMap_34.97.tar.gz 3986036 SHA256 46e9de558d5a7cb9f9db024ee59adaaee8fad28e5dbf1323cd619691f7ad8e53 SHA512 ddc43fe281af775946a8688805ec352431340a1e28ae0e8bd90dc8f2ef51435d03af73d3d90f2c0d04cf932d744acb43576bf89cd392e79f02393f9a6188598a WHIRLPOOL 21f73c14d4714024c7c68547da06037eef014e967c02ffc93f86887700366385d9edbfb67c67a648c314170bd2876c0ddb81e000c478138a706dd69f82e9d22a
DIST BBMap_35.92.tar.gz 4481029 SHA256 d15b1e42537f2cd947c4f1941e2be5a7d3584d632da5c0a372c84efed3d72ccb SHA512 d9d43d40d8791826ad9d9a639a2cf9f08fd92460d37a19564ca460b9c5ace988c91052bb4e7c7ca49eb807efa2d3869153bdd5615df0f5900d623a3aae930dc5 WHIRLPOOL 544e6227321fd70529b0c49c1e2029061368b3909baf17d76b09cc44b5af48dbe36835b0f82bd97f29a20eda16e0c7f5efcd79026ed95cd3a7f0596cb0512d7e
+DIST BBMap_36.02.tar.gz 4545396 SHA256 05dcee9a3b89f665449b6e48b4828557d6474d00616c8c035d4f73e02efe0760 SHA512 4e960bd8d3b665333bbcd2c8f1b74e5b40a8172ef3b92f0512f1f9ea26cd83116f1284147e3f2e4f7340f7fb472159b47442c082336d3c45bf42ecb99f911fad WHIRLPOOL f4ba6bd9d7153b62f52a0f717074664ac943853ea1f1806cd80273cb9026a9cee1a4b4f5194f9a4b4135de85e0072c8c92c22a12366e6308ed49263d5e1c6e70
diff --git a/sci-biology/bcftools/bcftools-1.2.ebuild b/sci-biology/bcftools/bcftools-1.2.ebuild
index 318dbc9d9..8c60b81c4 100644
--- a/sci-biology/bcftools/bcftools-1.2.ebuild
+++ b/sci-biology/bcftools/bcftools-1.2.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
# $Id$
@@ -21,10 +21,10 @@ RDEPEND="${DEPEND}"
src_prepare(){
sed -e "s@gcc@$(tc-getCC)@" \
- -e 's#prefix = /usr/local#prefix = /usr#' \
+ -e 's#prefix = /usr/local#prefix = "${EPREFIX}"/usr#' \
-e "s@CFLAGS = -g -Wall -Wc++-compat -O2@#CFLAGS = ${CFLAGS}@" -i Makefile || die
sed -e "s@gcc@$(tc-getCC)@" \
- -e 's#prefix = /usr/local#prefix = /usr#' \
+ -e 's#prefix = /usr/local#prefix = "${EPREFIX}"/usr#' \
-e "s@CFLAGS = -g -Wall -O2@#CFLAGS = ${CFLAGS}@" -i htslib-*/Makefile || die
}
diff --git a/sci-biology/biopieces/biopieces-0.51.ebuild b/sci-biology/biopieces/biopieces-0.51.ebuild
index ed5a25108..f3f407974 100644
--- a/sci-biology/biopieces/biopieces-0.51.ebuild
+++ b/sci-biology/biopieces/biopieces-0.51.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
# $Id$
@@ -6,7 +6,7 @@ EAPI=5
PYTHON_COMPAT=( python2_7 )
-USE_RUBY="ruby19"
+USE_RUBY="ruby20 ruby21"
if [ "$PV" == "9999" ]; then
ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
@@ -19,7 +19,7 @@ fi
inherit ruby-fakegem python-single-r1
-DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
+DESCRIPTION="Trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
HOMEPAGE="http://code.google.com/p/biopieces"
SRC_URI=""
@@ -67,6 +67,6 @@ RDEPEND="${CDEPEND}
sci-biology/bowtie
sci-biology/bwa
sci-biology/velvet
- sci-biology/idba
sci-biology/Ray
sci-biology/scan_for_matches"
+# sci-biology/idba
diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild
index ed5a25108..f3f407974 100644
--- a/sci-biology/biopieces/biopieces-9999.ebuild
+++ b/sci-biology/biopieces/biopieces-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
# $Id$
@@ -6,7 +6,7 @@ EAPI=5
PYTHON_COMPAT=( python2_7 )
-USE_RUBY="ruby19"
+USE_RUBY="ruby20 ruby21"
if [ "$PV" == "9999" ]; then
ESVN_REPO_URI="http://biopieces.googlecode.com/svn/trunk"
@@ -19,7 +19,7 @@ fi
inherit ruby-fakegem python-single-r1
-DESCRIPTION="Toolkit to find and trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
+DESCRIPTION="Trim adaptors, plot read lengths, qualities, map reads and submit to GenBank"
HOMEPAGE="http://code.google.com/p/biopieces"
SRC_URI=""
@@ -67,6 +67,6 @@ RDEPEND="${CDEPEND}
sci-biology/bowtie
sci-biology/bwa
sci-biology/velvet
- sci-biology/idba
sci-biology/Ray
sci-biology/scan_for_matches"
+# sci-biology/idba
diff --git a/sci-biology/biopieces/metadata.xml b/sci-biology/biopieces/metadata.xml
index 1699e58b2..f68a1b6fa 100644
--- a/sci-biology/biopieces/metadata.xml
+++ b/sci-biology/biopieces/metadata.xml
@@ -5,7 +5,7 @@
<email>mmokrejs@fold.natur.cuni.cz</email>
<name>Martin Mokrejs</name>
</maintainer>
-<maintainer type="project">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-9999.ebuild
index ca4ff2854..e651b6e22 100644
--- a/sci-biology/blasr/blasr-9999.ebuild
+++ b/sci-biology/blasr/blasr-9999.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
-MY_HASH=885c33a
-
inherit git-r3
DESCRIPTION="The PacBio long read aligner"
@@ -16,13 +14,21 @@ EGIT_REPO_URI="https://github.com/PacificBiosciences/blasr.git"
LICENSE="blasr"
SLOT="0"
-IUSE=""
+IUSE="hdf5"
KEYWORDS=""
-DEPEND="sci-libs/hdf5[cxx]"
+DEPEND="hdf5? ( >=sci-libs/hdf5-1.8.12[cxx] )" # needs H5Cpp.h
RDEPEND=""
-S="${WORKDIR}/blasr-${MY_HASH}"
+S="${WORKDIR}/blasr-9999"
+
+src_configure(){
+ if use hdf5; then \
+ python ./configure.py --shared --sub --no-pbbam HDF5_INCLUDE="${EPREFIX}"/usr/include HDF5_LIB="${EPREFIX}"/usr/lib64 || die
+ else
+ python ./configure.py --shared --sub --no-pbbam || die
+ fi
+}
src_install() {
dodir /usr/bin
diff --git a/sci-biology/grappa/grappa-2.0.ebuild b/sci-biology/grappa/grappa-2.0.ebuild
index cf0e06e0e..b07fb04be 100644
--- a/sci-biology/grappa/grappa-2.0.ebuild
+++ b/sci-biology/grappa/grappa-2.0.ebuild
@@ -23,6 +23,7 @@ src_prepare() {
src_install() {
dobin grappa
dosym grappa /usr/bin/invdist
- dosym grappa /usr/bin/distmat
+ # avoid file collision with emboss and rename distmat to distmat_grappa
+ dosym grappa /usr/bin/distmat_grappa
dodoc README
}
diff --git a/sci-biology/jannovar-bin/Manifest b/sci-biology/jannovar-bin/Manifest
new file mode 100644
index 000000000..795b27062
--- /dev/null
+++ b/sci-biology/jannovar-bin/Manifest
@@ -0,0 +1,2 @@
+DIST jannovar-cli-0.16.jar 9876562 SHA256 ed2392921fee745d9003af7eabbe5b2ed875e745a6ff10c8d7eff80a4206f2b7 SHA512 f5f639cc037e3b9659d290bf7953b82d5639d85708f3c96116045d4c030d24dca43bde3b2e5be543dd0e87305b1d70f94df5df6138299a49cc8c52a50076aef2 WHIRLPOOL bf3a75fa8d05e9019df4468f58b198b445dd7cca6d761b1073703c19583c2e87145cd18358c90d90b758a6948a198393e896c5ef8237de095ab1e7db6a4ae931
+DIST jped-cli-0.16.jar 9890813 SHA256 2f1e5b60c8f82fdb3a38dd9e876e281bca39942d880819e13dcc113f0957e27b SHA512 ee3b7e024fe376d5bec997f8b01c3ee8eac1bb48be160e66097d925387cc065418d90e8f3ca662866ea48573c5d3c4770e8a70be13c735e1ae62b5efe6cf8454 WHIRLPOOL 441c768d5e459961c71fb08f98e2e8209212420ae8ed70c422b9eba39d59d7040099d68315ca8c8d54660e515b562644eaacabb2994adf1113fb69f337faef7e
diff --git a/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
new file mode 100644
index 000000000..4d56e6586
--- /dev/null
+++ b/sci-biology/jannovar-bin/jannovar-bin-0.16.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2
+
+DESCRIPTION="Exome annotation tool"
+HOMEPAGE="http://compbio.charite.de
+ https://github.com/charite/jannovar"
+SRC_URI="https://github.com/charite/jannovar/releases/download/v${PV}/jannovar-cli-${PV}.jar
+ https://repo1.maven.org/maven2/de/charite/compbio/jped-cli/${PV}/jped-cli-${PV}.jar"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=">=virtual/jdk-1.6"
+RDEPEND=">=virtual/jre-1.6"
+
+S="${WORKDIR}"
+
+src_install(){
+ java-pkg_newjar "${DISTDIR}"/jannovar-cli-"${PV}".jar jannovar-cli.jar
+ java-pkg_dolauncher jannovar-cli-bin --jar jannovar-cli.jar
+ java-pkg_newjar "${DISTDIR}"/jped-cli-"${PV}".jar jped-cli.jar
+ java-pkg_dolauncher jped-cli-bin --jar jped-cli.jar
+}
diff --git a/sci-biology/jannovar-bin/metadata.xml b/sci-biology/jannovar-bin/metadata.xml
new file mode 100644
index 000000000..1699e58b2
--- /dev/null
+++ b/sci-biology/jannovar-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/jannovar/Manifest b/sci-biology/jannovar/Manifest
new file mode 100644
index 000000000..9a933661b
--- /dev/null
+++ b/sci-biology/jannovar/Manifest
@@ -0,0 +1 @@
+DIST jannovar-0.16.tar.gz 1025738 SHA256 e92d5dafc4157c40d3ddc2d96fb6b95971cf96e06abab3be2667c55558f41d20 SHA512 27a80bbce8e2536c21229093c0973138ff28a60404346d74c9f569a0dca0371e7d49c49e3dde3c788d88aa3f18285302b9525fd5b97c1f57101e4842071372f1 WHIRLPOOL c032065667f8f9f24fd4782a8dd656c50eb30d328cd23093ed22b13a7dc0fe6b3eef4219fd2edfd8addd8881c6dcd9a6e0f15b660800a2ae7609c83bfef3d6a7
diff --git a/sci-biology/jannovar/jannovar-0.16.ebuild b/sci-biology/jannovar/jannovar-0.16.ebuild
new file mode 100644
index 000000000..c67b78924
--- /dev/null
+++ b/sci-biology/jannovar/jannovar-0.16.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 java-pkg-2
+
+DESCRIPTION="Exome annotation tool"
+HOMEPAGE="http://compbio.charite.de/contao/index.php/jannovar.html"
+SRC_URI="https://github.com/charite/jannovar/archive/v0.16.tar.gz -> ${P}.tar.gz"
+
+# https://github.com/charite/jannovar
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=">=virtual/jdk-1.6
+ dev-java/maven-bin:*"
+RDEPEND=">=virtual/jre-1.6"
+
+# TODO: set a proxy because it downloads data during compile step
+# http://jannovar.readthedocs.io/en/master/install.html
+# see https://github.com/charite/jannovar/issues/218
+src_compile(){
+ mvn package -Dmaven.test.skip.exec=true -DskipTests=true || die
+}
+
+src_install(){
+ mvn install -Dmaven.test.skip.exec=true || die
+ java-pkg_dojar jannovar-cli.jar
+ java-pkg_dolauncher jannovar-cli --jar jannovar-cli.jar
+ java-pkg_dojar jped-cli.jar
+ java-pkg_dolauncher jped-cli --jar jped-cli.jar
+}
diff --git a/sci-biology/jannovar/metadata.xml b/sci-biology/jannovar/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/jannovar/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/prokka/prokka-1.11.ebuild b/sci-biology/prokka/prokka-1.11.ebuild
index 7b16d886b..5a5baca9a 100644
--- a/sci-biology/prokka/prokka-1.11.ebuild
+++ b/sci-biology/prokka/prokka-1.11.ebuild
@@ -19,7 +19,7 @@ RDEPEND="${DEPEND}
sys-process/parallel
sci-biology/bioperl
sci-biology/prodigal
- sci-biology/ncbi-tools++ || ( sci-biology/ncbi-blast+ )
+ || ( sci-biology/ncbi-tools++ sci-biology/ncbi-blast+ )
sci-biology/hmmer
sci-biology/infernal
sci-biology/exonerate