commit: b79af8f82794f511181ab43aa0c20871a4d39723 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Jan 7 20:42:05 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Jan 7 20:42:05 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b79af8f8
sci-biology/blue: Initial ebuild, does not install the *.exe.so files. Do we need them? --- sci-biology/Atlas/Atlas-2005.ebuild | 18 ++++ sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild | 22 +++++ sci-biology/CAutils/CAutils-20120126.ebuild | 20 ++++ sci-biology/InterMine/InterMine-0.98.ebuild | 3 + sci-biology/MochiView/MochiView-1.45.ebuild | 18 ++++ .../ampliconnoise/ampliconnoise-1.27.ebuild | 20 ++++ sci-biology/bioperl/bioperl-1.6.901.ebuild | 81 ++++++++++++++++ sci-biology/bioperl/metadata.xml | 5 + sci-biology/blue/ChangeLog | 10 ++ sci-biology/blue/blue-1.1.2.ebuild | 31 ++++++ sci-biology/blue/metadata.xml | 9 ++ sci-biology/ePCR/ePCR-2.3.12.ebuild | 34 +++++++ sci-biology/ePCR/files/config.mk.patch | 18 ++++ sci-biology/est2assembly/est2assembly-1.08.ebuild | 26 +++++ sci-biology/jigsaw/jigsaw-3.2.10.ebuild | 2 + sci-biology/pb-honey/pb-honey-14.1.15.ebuild | 25 +++++ sci-biology/pb-jelly/pb-jelly-14.1.14.ebuild | 22 +++++ sci-biology/primerD/primerD-1.0.0.ebuild | 3 + sci-biology/pvmsx/metadata.xml | 9 ++ sci-biology/pvmsx/pvmsx-0.1.ebuild | 46 +++++++++ .../tigr-closure/tigr-closure-20080106.ebuild | 66 +++++++++++++ sci-biology/ucsc-genome-browser/metadata.xml | 12 +++ .../ucsc-genome-browser-260.ebuild | 106 +++++++++++++++++++++ 23 files changed, 606 insertions(+) diff --git a/sci-biology/Atlas/Atlas-2005.ebuild b/sci-biology/Atlas/Atlas-2005.ebuild new file mode 100644 index 0000000..8400820 --- /dev/null +++ b/sci-biology/Atlas/Atlas-2005.ebuild @@ -0,0 +1,18 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Atlas Whole Genome Assembly Suite" +HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite"; +SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas-src.tgz"; +# https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas2005-linux.tgz + +LICENSE="" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" diff --git a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild new file mode 100644 index 0000000..b918714 --- /dev/null +++ b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Close gaps using BWA-identified reads and reassemble using Phrap, Newbler, Velvet, compare by cross_match" +HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-gapfill"; +SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/ATLAS_GapFill_V2.2_release.tar.bz2"; + +LICENSE="" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +# is there an ebuild for newbler? +DEPEND="dev-lang/perl + (sys-cluster/torque || sys/cluster/openpbs) + sci-biology/phrap + sci-biology/bwa + sci-biology/velvet" +RDEPEND="${DEPEND}" diff --git a/sci-biology/CAutils/CAutils-20120126.ebuild b/sci-biology/CAutils/CAutils-20120126.ebuild new file mode 100644 index 0000000..7b1ca7b --- /dev/null +++ b/sci-biology/CAutils/CAutils-20120126.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +DESCRIPTION="Additional utilities for Celera assembler (wgs-assembler) from UMD" +HOMEPAGE="http://www.cbcb.umd.edu/research/CeleraAssembler.shtml"; +SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/CAutils.tar.gz"; + +LICENSE="" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + dev-lang/perl" + +# is partially included in amos-3.1.0 diff --git a/sci-biology/InterMine/InterMine-0.98.ebuild b/sci-biology/InterMine/InterMine-0.98.ebuild new file mode 100644 index 0000000..a06fba7 --- /dev/null +++ b/sci-biology/InterMine/InterMine-0.98.ebuild @@ -0,0 +1,3 @@ +http://intermine.org/ +svn co svn://subversion.flymine.org/branches/intermine_0_98 +LGPL-3 diff --git a/sci-biology/MochiView/MochiView-1.45.ebuild b/sci-biology/MochiView/MochiView-1.45.ebuild new file mode 100644 index 0000000..5e9344a --- /dev/null +++ b/sci-biology/MochiView/MochiView-1.45.ebuild @@ -0,0 +1,18 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +DESCRIPTION="" +HOMEPAGE="" +SRC_URI="" + +LICENSE="" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + diff --git a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild new file mode 100644 index 0000000..984b7a6 --- /dev/null +++ b/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=4 + +DESCRIPTION="Noise removal from pyrosequenced amplicons" +HOMEPAGE="http://code.google.com/p/ampliconnoise/"; +SRC_URI="http://ampliconnoise.googlecode.com/files/AmpliconNoiseV"${PV}".tar.gz + http://ampliconnoise.googlecode.com/files/TutorialV1.22.tar.gz + http://ampliconnoise.googlecode.com/files/DiversityEstimates.tar.gz"; + +LICENSE="LGPL" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + diff --git a/sci-biology/bioperl/bioperl-1.6.901.ebuild b/sci-biology/bioperl/bioperl-1.6.901.ebuild new file mode 100644 index 0000000..98d0763 --- /dev/null +++ b/sci-biology/bioperl/bioperl-1.6.901.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.6.1.ebuild,v 1.3 2009/10/02 14:51:51 weaver Exp $ + +EAPI="2" + +inherit perl-module + +SUBPROJECTS="+db +network +run" +MIN_PV="1.6" + +DESCRIPTION="Perl tools for bioinformatics - Core modules" +HOMEPAGE="http://www.bioperl.org/"; +# SRC_URI="http://www.bioperl.org/DIST/BioPerl-${PV}.tar.bz2"; +SRC_URI="http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-${PV}.tar.gz"; + +LICENSE="Artistic GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="-minimal graphviz sqlite ${SUBPROJECTS}" + +CDEPEND=">=perl-core/Module-Build-0.380.0 + dev-perl/Data-Stag + dev-perl/libwww-perl + !minimal? ( + dev-perl/Ace + dev-perl/Spreadsheet-ParseExcel + dev-perl/Spreadsheet-WriteExcel + >=dev-perl/XML-SAX-0.15 + dev-perl/Graph + dev-perl/SOAP-Lite + dev-perl/Array-Compare + dev-perl/SVG + dev-perl/XML-Simple + dev-perl/XML-Parser + dev-perl/XML-Twig + >=dev-perl/HTML-Parser-3.60 + >=dev-perl/XML-Writer-0.4 + dev-perl/Clone + dev-perl/XML-DOM + dev-perl/set-scalar + dev-perl/XML-XPath + dev-perl/XML-DOM-XPath + dev-perl/Algorithm-Munkres + dev-perl/Data-Stag + dev-perl/Math-Random + dev-perl/PostScript + dev-perl/Convert-Binary-C + dev-perl/SVG-Graph + dev-perl/IO-String + dev-perl/Class-Inspector + dev-perl/Sort-Naturally + ) + graphviz? ( dev-perl/GraphViz ) + sqlite? ( dev-perl/DBD-SQLite )" +DEPEND="virtual/perl-Module-Build + ${CDEPEND}" +# In perl-overlay +# >=virtual/perl-ExtUtils-Manifest-1.52 (to CDEPEND?) +# >=perl-CPAN/perl-CPAN-1.81 +RDEPEND="${CDEPEND}" +PDEPEND="!minimal? ( dev-perl/Bio-ASN1-EntrezGene ) + db? ( >=sci-biology/bioperl-db-${MIN_PV} ) + network? ( >=sci-biology/bioperl-network-${MIN_PV} ) + run? ( >=sci-biology/bioperl-run-${MIN_PV} )" + +S="${WORKDIR}/BioPerl-${PV}" + +src_configure() { + sed -i -e '/add_post_install_script.*symlink_script.pl/d' \ + -e "/'CPAN' *=> *1.81/d" \ + -e "/'ExtUtils::Manifest' *=> *'1.52'/d" "${S}/Build.PL" || die + + if use minimal && use graphviz; then die "USE flags minimal and graphviz cannot be used together"; fi + perl-module_src_configure +} + +src_install() { + mydoc="AUTHORS BUGS FAQ" + perl-module_src_install +} diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml new file mode 100644 index 0000000..d464821 --- /dev/null +++ b/sci-biology/bioperl/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/blue/ChangeLog b/sci-biology/blue/ChangeLog new file mode 100644 index 0000000..7c74563 --- /dev/null +++ b/sci-biology/blue/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/blue +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*blue-1.1.2 (07 Jan 2015) + + 07 Jan 2015; Martin Mokrejs <[email protected]> +blue-1.1.2.ebuild, + +metadata.xml: + Initial ebuild, does not install the *.exe.so files. Do we need them? + diff --git a/sci-biology/blue/blue-1.1.2.ebuild b/sci-biology/blue/blue-1.1.2.ebuild new file mode 100644 index 0000000..52ca614 --- /dev/null +++ b/sci-biology/blue/blue-1.1.2.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Error corrector for Illummina and Roche/454 able to also fix insertions and deletions" +HOMEPAGE="http://www.csiro.au/Outcomes/ICT-and-Services/Software/Blue.aspx"; +SRC_URI="http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Linux112.ashx -> "${P}".tar.gz + http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Correcting_reads_with_Blue.ashx -> Correcting_reads_with_Blue.pdf" + +LICENSE="GPL" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="dev-lang/mono" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/Linux + +src_compile(){ + Blue/compile.sh || die + Tessel/compile.sh || die + GenerateMerPairs/compile.sh || die +} + +src_install(){ + dobin Tessel.exe GenerateMerPairs.exe Blue.exe + # BUG: probably have to install also the *.exe.so files +} diff --git a/sci-biology/blue/metadata.xml b/sci-biology/blue/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/blue/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/ePCR/ePCR-2.3.12.ebuild b/sci-biology/ePCR/ePCR-2.3.12.ebuild new file mode 100644 index 0000000..8e71c90 --- /dev/null +++ b/sci-biology/ePCR/ePCR-2.3.12.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +inherit eutils + +DESCRIPTION="Search for sub-sequences matching PCR primers with correct order, orientation, and spacing" +HOMEPAGE="http://www.ncbi.nlm.nih.gov/projects/e-pcr/"; +SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/pub/schuler/e-PCR/e-PCR-"${PV}"-src.tar.gz"; + +LICENSE="" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +S=${WORKDIR}"/e-PCR-"${PV} + +src_prepare(){ + epatch ${FILESDIR}"/config.mk.patch" +} + +src_compile(){ + make -j1 srcdir=${S} objdir=${S} || die "make -j1 failed" +} + +src_install(){ + dobin e-PCR famap fahash re-PCR + dodoc README.TXT +} diff --git a/sci-biology/ePCR/files/config.mk.patch b/sci-biology/ePCR/files/config.mk.patch new file mode 100644 index 0000000..1960b43 --- /dev/null +++ b/sci-biology/ePCR/files/config.mk.patch @@ -0,0 +1,18 @@ +--- stand/config.mk.ori 2012-01-16 17:38:11.000000000 +0100 ++++ stand/config.mk 2012-01-16 17:39:12.000000000 +0100 +@@ -52,11 +52,11 @@ + + ######################################################################### + # GNU compiler flags +-CC = gcc +-CXX = g++ +-CXXFLAGS = -I$(srcdir) -I$(INCDIR) $(CC_FLAGS) $(PART_CXXFLAGS) \ ++#CC = gcc ++#CXX = g++ ++CXXFLAGS = -I$(srcdir) -I$(INCDIR) -I`pwd` \ + -DDEALLOCATE=0 $(LF64CCFLAGS) $(VERSION_FLAGS) -DSTANDALONE=1 +-LDFLAGS = $(LD_FLAGS) $(LF64LDFLAGS) -L$(tgtdir) -L$(LIBDIR) $(PART_LDFLAGS) ++LDFLAGS = $(LF64LDFLAGS) -L$(tgtdir) -L$(LIBDIR) + # $(PART_PRELIBS) $(LIBS:%=-l%) $(PART_POSTLIBS) + + LF64CCFLAGS = `getconf LFS_CFLAGS` diff --git a/sci-biology/est2assembly/est2assembly-1.08.ebuild b/sci-biology/est2assembly/est2assembly-1.08.ebuild new file mode 100644 index 0000000..72fcd5d --- /dev/null +++ b/sci-biology/est2assembly/est2assembly-1.08.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display" +HOMEPAGE="http://code.google.com/p/est2assembly/"; +SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_1.08.tar.gz"; + +LICENSE="GPL-v3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="dev-lang/perl + app-portage/g-cpan + perl-gcpan/Time-Progress + sci-biology/fasta + sci-biology/ssaha2 + sci-biology/mira + sci-biology/emboss + sci-biology/bioperl + app-arch/pbzip2" +RDEPEND="${DEPEND}" + diff --git a/sci-biology/jigsaw/jigsaw-3.2.10.ebuild b/sci-biology/jigsaw/jigsaw-3.2.10.ebuild new file mode 100644 index 0000000..5f85fbf --- /dev/null +++ b/sci-biology/jigsaw/jigsaw-3.2.10.ebuild @@ -0,0 +1,2 @@ +http://www.cbcb.umd.edu/software/jigsaw/ +http://cbcb.umd.edu/software/jigsaw/jigsaw-3.2.10.tar.gz diff --git a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild new file mode 100644 index 0000000..2ba4b1a --- /dev/null +++ b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Structural variant identification (SNV) using long reads (over 10kbp)" +HOMEPAGE="https://www.hgsc.bcm.edu/software/honey"; +SRC_URI="http://sourceforge.net/projects/pb-jelly/files/PBHoney/PBHoney_14.1.15.tgz"; + +LICENSE="" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="sci-biology/samtools + sci-biology/blasr + sci-biology/pysam + dev-python/h5py + dev-python/numpy" +RDEPEND="${DEPEND}" diff --git a/sci-biology/pb-jelly/pb-jelly-14.1.14.ebuild b/sci-biology/pb-jelly/pb-jelly-14.1.14.ebuild new file mode 100644 index 0000000..0c65915 --- /dev/null +++ b/sci-biology/pb-jelly/pb-jelly-14.1.14.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Close gaps using PacBio RS or 454 FLX+ reads" +HOMEPAGE="https://www.hgsc.bcm.edu/software/jelly"; +SRC_URI="http://sourceforge.net/projects/pb-jelly/files/PBJelly/PBJelly_14.1.14.tgz"; + +LICENSE="" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="sci-biology/blasr + dev-python/networkx-1.1" # upstream says "Versions past v1.1 have been shown to have many issues." +RDEPEND="${DEPEND}" diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild b/sci-biology/primerD/primerD-1.0.0.ebuild new file mode 100644 index 0000000..764d698 --- /dev/null +++ b/sci-biology/primerD/primerD-1.0.0.ebuild @@ -0,0 +1,3 @@ +"A program to design denegerate primer pairs" +http://mblab.wustl.edu/software.html +http://mblab.wustl.edu/software/download/primerD.tar.gz diff --git a/sci-biology/pvmsx/metadata.xml b/sci-biology/pvmsx/metadata.xml new file mode 100644 index 0000000..07b5255 --- /dev/null +++ b/sci-biology/pvmsx/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/pvmsx/pvmsx-0.1.ebuild b/sci-biology/pvmsx/pvmsx-0.1.ebuild new file mode 100644 index 0000000..1983f6b --- /dev/null +++ b/sci-biology/pvmsx/pvmsx-0.1.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +DESCRIPTION="parallel multi-FASTA file processing tool using PVM from TIGR Gene Indices project tools, an alternative to psx" +HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"; +SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz + ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"; + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="pvm" + +DEPEND="pvm? ( sys-cluster/pvm )" +RDEPEND="${DEPEND}" + +S=${WORKDIR} + +src_unpack(){ + mkdir ${PN} || die + cd ${PN} || die "Failed to chdir" + unpack ${PN}.tar.gz || die +} + +src_prepare() { + # we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h + sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed" + sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die + sed -i "s#-I-#-iquote#" ${S}/${PN}/Makefile + cd ${PN} || die + ln -s ../cdbfasta/gcl . || die "Cannot make a softlink" +} + +src_compile() { + cd ${PN} || die + emake || die "emake failed in "${S}"/${PN}" +} + +src_install() { + cd ${PN} || die + dobin ${PN} || die "Failed to install ${PN} binary" + newdoc README README.${PN} +} diff --git a/sci-biology/tigr-closure/tigr-closure-20080106.ebuild b/sci-biology/tigr-closure/tigr-closure-20080106.ebuild new file mode 100644 index 0000000..e4a2421 --- /dev/null +++ b/sci-biology/tigr-closure/tigr-closure-20080106.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +inherit perl-module + +DESCRIPTION="TIGR closure tools for the assembly/finishing stage of DNA sequencing projects" +HOMEPAGE="http://tigr-closure.sourceforge.net/"; +# http://tigr-closure.svn.sourceforge.net/tigr-closure/ +SRC_URI="tigr-closure-svn-20080106.tar.gz" + +LICENSE="" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="" + +DEPEND="dev-lang/perl" +RDEPEND="" + +src_compile() { + cd TIGR + # install the two *.pm files into our perl path? + cd .. + + # Closure Work Order Processing (CWP - CLOVER) + # clover and oats + cd ${WORKDIR}/CWPSystem/trunk/ + # needs TIGR/EUIDService.pm in PERL paths + make dist + # how to install the files from install/ ? + cd ../.. + + # + cd ScaffoldMgmt/trunk + make dist + # FIXME: unpack the .tar file into image during src_install() + cd ../.. + + # awfull + cd ClosureQC/trunk/ + mkdir sandbox + ${SANDBOX}=${WORKDIR}/sandbox + # have ./src/, ./doc, ./install, ./test/work/drivers, ./test/work/getqc, ./test/tmp + cd test + # ... + cd ../../.. + + # + cd ClosureReactionSystem/trunk + make BUILD=true + cd ../.. + + # some Java servlet? + cd AserverConsoleEJB3Hibernate + # huh? + cd ../.. +} + +src_install() { + cd ${WORKDIR}/SequenceTiling + dobin trunk/src/*.pl + cd trunk/src/TIGR/SequenceTiling/ + myinst="DESTDIR=${D}" + perl-module_src_install + # +} diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml new file mode 100644 index 0000000..18137f6 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/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> + <email>[email protected]</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci-biology</herd> + <use> + <flag name="server">Install genome browser Web application. If this flag is off, only libraries and utilities from the suite are installed.</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild new file mode 100644 index 0000000..ae00dd8 --- /dev/null +++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild @@ -0,0 +1,106 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild,v 1.1 2011/12/27 09:39:04 jlec Exp $ + +EAPI=4 + +inherit toolchain-funcs flag-o-matic webapp + +DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath" +HOMEPAGE="http://genome.ucsc.edu/"; +SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${PV}.zip"; + +LICENSE="blat" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="+mysql +server +static-libs" + +REQUIRED_USE="server? ( mysql )" + +WEBAPP_MANUAL_SLOT="yes" + +DEPEND=" + app-arch/unzip + !<sci-biology/ucsc-genome-browser-223 + mysql? ( virtual/mysql ) + server? ( virtual/httpd-cgi )" # TODO: test with other webservers +RDEPEND="${DEPEND}" + +S="${WORKDIR}/kent" + +src_prepare() { + use server && webapp_src_preinst + sed \ + -e 's/-Werror//' \ + -e "/COPT/s:=.*$:=${LDFLAGS}:g" \ + -e "s/CC=gcc/CC=$(tc-getCC) ${CFLAGS}/" \ + -e 's:${CC} ${COPT} ${CFLAGS}:${CC} ${CFLAGS}:g' \ + -i src/inc/common.mk src/hg/lib/makefile || die + find -name makefile -or -name cgi_build_rules.mk \ + | xargs sed -i \ + -e 's/-${USER}//g' \ + -e 's/-$(USER)//g' \ + -e 's:-O2::g' \ + -e 's:-ggdb::g' \ + -e 's:-pipe::g' || die + sed \ + -e 's:${DISTDIR}${BINDIR}:${BINDIR}:g' \ + -i src/hg/genePredToMafFrames/makefile || die +} + +src_compile() { + export MACHTYPE=${MACHTYPE/-*/} \ + BINDIR="${WORKDIR}/destdir/opt/${PN}/bin" \ + SCRIPTS="${WORKDIR}/destdir/opt/${PN}/cluster/scripts" \ + ENCODE_PIPELINE_BIN="${WORKDIR}/destdir/opt/${PN}/cluster/data/encode/pipeline/bin" \ + PATH="${BINDIR}:${PATH}" \ + STRIP="echo 'skipping strip' " + + export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none" + + use mysql && export MYSQLLIBS="-L${EROOT}usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \ + MYSQLINC="${ROOT}usr/include/mysql" + + use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \ + CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin" + + mkdir -p "$BINDIR" "$SCRIPTS" "$ENCODE_PIPELINE_BIN" || die + use server && mkdir -p "$CGI_BIN" "$DOCUMENTROOT" + + emake -C src clean + emake -C src/lib + emake -C src/jkOwnLib + emake -C src/utils/stringify + emake -C src blatSuite + if use mysql; then + emake -j1 -C src/hg utils + emake -j1 -C src utils + emake -C src libs userApps + if use server; then + emake -j1 -C src/hg + emake -j1 -C src + fi + fi +} + +src_install() { + use server && webapp_src_preinst + cp -ad "${WORKDIR}"/destdir/* "${D}" || die + use static-libs && dolib.a src/lib/${MACHTYPE/-*/}/*.a + echo "PATH=${EPREFIX}/opt/${PN}/bin" > "${S}/98${PN}" + doenvd "${S}/98${PN}" + + use server && webapp_postinst_txt en src/product/README.QuickStart + use server && webapp_src_install + + insinto "/usr/include/${PN}" + doins src/inc/*.h + insinto "/usr/share/${PN}" + doins -r src/product + keepdir "/usr/share/doc/${PF}" + find -name 'README*' -or -name '*.doc' | grep -v test | cpio -padv "${ED}/usr/share/doc/${PF}" || die +} + +pkg_postinst() { + use server && webapp_pkg_postinst +}
