commit: f291cafdf1bac38dea4e9781f08ee7cc171a6dc4 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Mar 29 13:00:21 2019 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Mar 29 13:00:21 2019 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f291cafd
sci-biology/augustus: version bump, fix awful Makefile's Do not require static libraries. Only bamtools are really needed. htslib is not needed. For bam2wig samtools-0.2 series is needed. I decided to blindly install some of the binaries created but not copied into `./bin/`. `src/Makefile` will gladly define mysql and sqlite together, probably a non-sense. We force mysql as we check for it first. Not sure if sqlite should be preferred. I documented in the augustus-3.3.2.ebuild other "forgotten" files, like gbrowse.conf and a template for gff2ps. I dropped `-O3` but left in `-ggdb` in the `CXXFLAGS`. https://github.com/Gaius-Augustus/Augustus/issues/14 https://github.com/Gaius-Augustus/Augustus/issues/50 https://github.com/Gaius-Augustus/Augustus/issues/51 https://github.com/Gaius-Augustus/Augustus/issues/52 https://github.com/Gaius-Augustus/Augustus/issues/53 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> sci-biology/augustus/augustus-3.3.2.ebuild | 115 +++++++++++++++++++++++++++++ sci-biology/augustus/augustus-3.3.ebuild | 70 ------------------ sci-biology/augustus/metadata.xml | 4 + 3 files changed, 119 insertions(+), 70 deletions(-) diff --git a/sci-biology/augustus/augustus-3.3.2.ebuild b/sci-biology/augustus/augustus-3.3.2.ebuild new file mode 100644 index 000000000..f28fb4e93 --- /dev/null +++ b/sci-biology/augustus/augustus-3.3.2.ebuild @@ -0,0 +1,115 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit eutils toolchain-funcs + +DESCRIPTION="Eukaryotic gene predictor" +HOMEPAGE="http://bioinf.uni-greifswald.de/augustus + https://github.com/Gaius-Augustus/Augustus"; +SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/3.3.2.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +# temporary drop in licensing scheme, see http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT +# http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT +# LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="bam2wig examples man mysql sqlite" + +RDEPEND=" + bam2wig? ( sci-biology/samtools:0.1-legacy ) + sci-biology/bamtools + >=sci-mathematics/lpsolve-5.5 + sci-libs/gsl + sci-libs/suitesparse + sqlite? ( dev-db/sqlite:3 ) + mysql? ( dev-db/mysql++ ) + >=dev-libs/boost-1.49.0 + sys-libs/zlib" +DEPEND="${RDEPEND} + sys-devel/flex" +S="${WORKDIR}/Augustus-${PV}" + +src_prepare() { + # TODO: do we need anything from the 2.5.5 patch? + # epatch "${FILESDIR}"/${P}-sane-build.patch + default + tc-export CC CXX + # lets respect upstream's wish and keep -ggdb + sed -e 's#-ggdb -O3#-ggdb#' -i src/Makefile || die + sed -e 's#TOOLDIR=$(HOME)/tools#TOOLDIR='"${EPREFIX}/usr/include#" \ + -i auxprogs/bam2wig/Makefile || die + sed -e "s#INCLUDES=#INCLUDES=-I${EPREFIX}/usr/include/bam-0.1-legacy #" \ + -i auxprogs/bam2wig/Makefile || die + # https://github.com/Gaius-Augustus/Augustus/issues/53 + sed -e 's#$(SAMTOOLS)/libbam.a $(HTSLIB)/libhts.a -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto#-lbam-0.1-legacy#' -i auxprogs/bam2wig/Makefile || die + sed -e 's#-lbz2 -llzma##' -i auxprogs/bam2wig/Makefile || die + # enable comparative gene prediction (CGP, needs c++11 compiler), + # this needs sci-mathematics/lpsolve + sed -e 's/^# COMPGENEPRED/COMPGENEPRED/' -i common.mk || die + # enable compressed gzip input + sed -e 's/^#ZIPINPUT/ZIPINPUT/' -i common.mk || die + # comparative (multi-species, CGP) AUGUSTUS with MySQL or SQLite + # supposedly pick only either a single-one + if use mysql; then + sed -e 's/^#MYSQL/MYSQL/' -i common.mk || die + elif use sqlite; then + # comparative (mutli-species, CGP) AUGUSTUS with SQLite + sed -e 's/^# SQLITE/SQLITE/' -i common.mk || die + fi + # respect $EPREFIX in all Makefile's + find . -name Makefile | while read f; do \ + sed -s "s#/usr/include#${EPREFIX}/usr/include#g" -i $f || die; + done +} + +src_compile() { + emake clean && default + + # compile stuff not compiled by default + # https://github.com/Gaius-Augustus/Augustus/issues/52 + cd auxprogs/aln2wig || die + emake +} + +src_install() { + dobin bin/* + + exeinto /usr/libexec/${PN} + doexe scripts/*.{pl,pm,py} scripts/checkUTR + insinto /usr/libexec/${PN} + doins scripts/*.conf + + insinto /usr/share/${PN} + doins -r config + + echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}" + doenvd "${S}/99${PN}" + + insinto /usr/libexec/${PN}/gbrowse + doins scripts/gbrowse.conf + insinto /usr/libexec/${PN}/gfftools + doins scripts/gff2ps_mycustom # config setting + + dodoc README.md README-cgp.txt HISTORY.TXT auxprogs/homGeneMapping/README.TXT + dodoc -r docs/*.{pdf,txt} + + if use examples; then + insinto /usr/share/${PN}/ + doins -r docs/tutorial examples + fi + + use man && doman mansrc/*.1 + + # install stuff not compiled but not written into bin/ + # https://github.com/Gaius-Augustus/Augustus/issues/14 + dobin auxprogs/utrrnaseq/Debug/utrrnaseq + dodoc auxprogs/utrrnaseq/doc/reference.pdf + # https://github.com/Gaius-Augustus/Augustus/issues/51 + dobin auxprogs/checkTargetSortedness/checkTargetSortedness \ + auxprogs/compileSpliceCands/compileSpliceCands + + # ./augustus-training/ contains web application and setup +} diff --git a/sci-biology/augustus/augustus-3.3.ebuild b/sci-biology/augustus/augustus-3.3.ebuild deleted file mode 100644 index b2b19a04e..000000000 --- a/sci-biology/augustus/augustus-3.3.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Eukaryotic gene predictor" -HOMEPAGE="http://augustus.gobics.de/"; -SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/${P}.tar.gz"; - -LICENSE="GPL-3" -# temporary drop in licensing scheme, see http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT -# http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT -# LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="examples" - -# TODO: provide USE for mysql and sqlite, edit src/Makefile to reflect paths -# and common.mk -RDEPEND=" - sci-mathematics/lpsolve - sci-libs/gsl - dev-libs/boost - sys-libs/zlib" -DEPEND="${RDEPEND} - sys-devel/flex" -S="${WORKDIR}/${PN}" - -src_prepare() { - # TODO: do we need anything from the 2.5.5 patch? - # epatch "${FILESDIR}"/${P}-sane-build.patch - tc-export CC CXX - sed -e 's/ -O3//g' -i src/Makefile || die - # enable comparative gene prediction (needs c++11 compiler), - # this needs sci-mathematics/lpsolve - sed -e 's/^# COMPGENEPRED/COMPGENEPRED/' -i common.mk || die - # respect $EPREFIX at src/Makefile, auxprogs/bam2hints/Makefile, more? - find . -name Makefile | while read f; do \ - sed -s 's#/usr/include#${EPREFIX}/usr/include#' -i $f || die; - done -} - -src_compile() { - emake clean && default -} - -src_install() { - dobin bin/* -# dobin src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign} - - exeinto /usr/libexec/${PN} - doexe scripts/*.p* - insinto /usr/libexec/${PN} - doins scripts/*.conf - - insinto /usr/share/${PN} - doins -r config - - echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}" - doenvd "${S}/99${PN}" - - dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt} - - if use examples; then - insinto /usr/share/${PN}/ - doins -r docs/tutorial examples - fi -} diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml index 8417d1580..6b4a3e5b5 100644 --- a/sci-biology/augustus/metadata.xml +++ b/sci-biology/augustus/metadata.xml @@ -5,4 +5,8 @@ <email>sci-biol...@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <use> + <flag name="man">install preformatted manual pages</flag> + <flag name="bam2wig">compile and install bam2wig conversion utility</flag> + </use> </pkgmetadata>
