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