[gentoo-commits] proj/sci:master commit in: sci-biology/augustus/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

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-biology@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>