diff options
Diffstat (limited to 'sci-biology')
93 files changed, 1485 insertions, 587 deletions
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 |