commit: e1a3b476590c330602639ad79e5130c1c8864c74 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Oct 4 08:10:18 2016 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Oct 4 08:10:18 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e1a3b476
sci-biology/consed: this version now landed main tree, removing sci-biology/consed/consed-29.ebuild | 93 ------------------------------------- sci-biology/consed/metadata.xml | 12 ----- 2 files changed, 105 deletions(-) diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild deleted file mode 100644 index 002e007..0000000 --- a/sci-biology/consed/consed-29.ebuild +++ /dev/null @@ -1,93 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="A genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"; -SRC_URI=" - ${P}-sources.tar.gz - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=">=x11-libs/motif-2.3:0" -# it needs samtools-0.18 with khash.h -# This file was about sci-biology/samtools-1.2 time moved to sci-libs/htslib-1.2.1 -RDEPEND="${DEPEND} - <sci-biology/samtools-1.0 - >=sci-biology/samtools-0.1.18 - >=sci-biology/phred-000925 - >=sci-biology/phrap-1.080721 - dev-lang/perl" - -S="${WORKDIR}" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" - einfo "and place it in ${DISTDIR}," - einfo "obtain the file" - einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" - einfo "and place it in ${DISTDIR}" -} - -src_prepare() { - sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die - sed -i \ - -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \ - -e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \ - -e 's/CFLGS=/CFLGS= ${CFLAGS} /' \ - -e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/ -I/usr/include/htslib/#' "${S}/makefile" || die - sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die - sed \ - -e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \ - -i "${S}"/scripts/* || die -} - -src_compile() { - einfo "consed does not compile with >=sys-devel/gcc-4.6:* but 4.4.7 works" - default - emake -C misc/mktrace - emake -C misc/phd2fasta - (cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} - dobin scripts/* contributions/* - insinto /usr/lib/screenLibs - doins misc/*.{fa*,seq} - insinto /usr/share/${PN}/examples - doins -r \ - 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 - touch "${ED}"/etc/consedrc || die "Cannot create a file for system-wide settings" - doenvd "${S}/99consed" - sed \ - -e "s#/usr/local/genome#${EPREFIX}/usr#" \ - -i "${ED}"/usr/bin/{*.perl,phredPhrap,phredPhrapWithPhdBalls} || die - sed \ - -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' \ - -i "${ED}"/usr/bin/phredPhrap || die - sed \ - -e 's#/wt1/gordon/genome#/usr/bin#' \ - -i "${ED}"/usr/bin/fastq2Phrap.perl || die - dodoc README.txt *_announcement.txt -} - -pkg_postinst() { - einfo "Package documentation is available at" - einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"; -} diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml deleted file mode 100644 index 1699e58..0000000 --- a/sci-biology/consed/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 type="person"> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> -<maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata>
