commit: 3d70d539efdee4713fc377c55a0585791f965179 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Jul 23 00:13:48 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Jul 23 00:13:48 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3d70d539
sci-biology/consed-29.0: version bump Package-Manager: portage-2.2.18 sci-biology/consed/ChangeLog | 9 ++++ sci-biology/consed/consed-29.ebuild | 93 +++++++++++++++++++++++++++++++++++++ sci-biology/consed/metadata.xml | 9 ++++ 3 files changed, 111 insertions(+) diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog new file mode 100644 index 0000000..a580e1e --- /dev/null +++ b/sci-biology/consed/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/consed +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*consed-29 (23 Jul 2015) + + 23 Jul 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> +consed-29.ebuild, + +metadata.xml: + sci-biology/consed-29.0: version bump diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild new file mode 100644 index 0000000..c6e3cf9 --- /dev/null +++ b/sci-biology/consed/consed-29.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-27.ebuild,v 1.1 2014/10/26 16:13:23 jlec Exp $ + +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/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!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${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)" + emake + 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 + mkdir -p "${ED}"/etc/consedrc || die + touch "${ED}"/etc/consedrc || die + doenvd "${S}/99consed" || die + sed \ + -e "s#/usr/local/genome#${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 "${ED}"/usr/bin/fastq2Phrap.perl || die + dodoc README.txt *_announcement.txt || die +} + +pkg_postinst() { + einfo "Package documentation is available at" + einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"; +} diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/consed/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>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata>
