commit: 2c54fbea31de3d8b20ca965d780805fdf20dd018 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Wed Jan 7 20:42:52 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Jan 7 20:42:52 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2c54fbea
Revert "sci-biology/blue: Initial ebuild, does not install the *.exe.so files. Do we need them?" This reverts commit b79af8f82794f511181ab43aa0c20871a4d39723. --- 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 deletions(-) diff --git a/sci-biology/Atlas/Atlas-2005.ebuild b/sci-biology/Atlas/Atlas-2005.ebuild deleted file mode 100644 index 8400820..0000000 --- a/sci-biology/Atlas/Atlas-2005.ebuild +++ /dev/null @@ -1,18 +0,0 @@ -# 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 deleted file mode 100644 index b918714..0000000 --- a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# 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 deleted file mode 100644 index 7b1ca7b..0000000 --- a/sci-biology/CAutils/CAutils-20120126.ebuild +++ /dev/null @@ -1,20 +0,0 @@ -# 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 deleted file mode 100644 index a06fba7..0000000 --- a/sci-biology/InterMine/InterMine-0.98.ebuild +++ /dev/null @@ -1,3 +0,0 @@ -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 deleted file mode 100644 index 5e9344a..0000000 --- a/sci-biology/MochiView/MochiView-1.45.ebuild +++ /dev/null @@ -1,18 +0,0 @@ -# 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 deleted file mode 100644 index 984b7a6..0000000 --- a/sci-biology/ampliconnoise/ampliconnoise-1.27.ebuild +++ /dev/null @@ -1,20 +0,0 @@ -# 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 deleted file mode 100644 index 98d0763..0000000 --- a/sci-biology/bioperl/bioperl-1.6.901.ebuild +++ /dev/null @@ -1,81 +0,0 @@ -# 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 deleted file mode 100644 index d464821..0000000 --- a/sci-biology/bioperl/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?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 deleted file mode 100644 index 7c74563..0000000 --- a/sci-biology/blue/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# 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 deleted file mode 100644 index 52ca614..0000000 --- a/sci-biology/blue/blue-1.1.2.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# 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 deleted file mode 100644 index 2bc8930..0000000 --- a/sci-biology/blue/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ -<?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 deleted file mode 100644 index 8e71c90..0000000 --- a/sci-biology/ePCR/ePCR-2.3.12.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# 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=${S} || die "make -j1 failed" -} - -src_install(){ - dobin e-PCR famap fahash re-PCR - dodoc README.TXT -} diff --git a/sci-biology/ePCR/files/config.mk.patch b/sci-biology/ePCR/files/config.mk.patch deleted file mode 100644 index 1960b43..0000000 --- a/sci-biology/ePCR/files/config.mk.patch +++ /dev/null @@ -1,18 +0,0 @@ ---- stand/config.mk.ori 2012-01-16 17:38:11.000000000 +0100 -+++ stand/config.mk 2012-01-16 17:39:12.000000000 +0100 -@@ -52,11 +52,11 @@ - - ######################################################################### - # GNU compiler flags --CC = gcc --CXX = g++ --CXXFLAGS = -I$(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 deleted file mode 100644 index 72fcd5d..0000000 --- a/sci-biology/est2assembly/est2assembly-1.08.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# 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 deleted file mode 100644 index 5f85fbf..0000000 --- a/sci-biology/jigsaw/jigsaw-3.2.10.ebuild +++ /dev/null @@ -1,2 +0,0 @@ -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 deleted file mode 100644 index 2ba4b1a..0000000 --- a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# 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 deleted file mode 100644 index 0c65915..0000000 --- a/sci-biology/pb-jelly/pb-jelly-14.1.14.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# 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 deleted file mode 100644 index 764d698..0000000 --- a/sci-biology/primerD/primerD-1.0.0.ebuild +++ /dev/null @@ -1,3 +0,0 @@ -"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 deleted file mode 100644 index 07b5255..0000000 --- a/sci-biology/pvmsx/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ -<?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 deleted file mode 100644 index 1983f6b..0000000 --- a/sci-biology/pvmsx/pvmsx-0.1.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# 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 deleted file mode 100644 index e4a2421..0000000 --- a/sci-biology/tigr-closure/tigr-closure-20080106.ebuild +++ /dev/null @@ -1,66 +0,0 @@ -# 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 deleted file mode 100644 index 18137f6..0000000 --- a/sci-biology/ucsc-genome-browser/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?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 deleted file mode 100644 index ae00dd8..0000000 --- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild +++ /dev/null @@ -1,106 +0,0 @@ -# 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 -}
