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

["Justin Lecher" <jlec@gentoo.org>]

commit:     a4b81acad6cf95e5d00067340180ff69a07d5a5f
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 22 07:56:27 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep 22 07:56:27 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a4b81aca

sci-biology/sra_sdk: Bump to EAPI=5

Package-Manager: portage-2.2.21
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild  |  66 --------------------
 sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild  | 100 ------------------------------
 sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild |  37 ++++++-----
 3 files changed, 18 insertions(+), 185 deletions(-)

diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild b/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
deleted file mode 100644
index f91cf38..0000000
--- a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-inherit eutils
-
-W="${WORKDIR}"/"${P}"
-
-DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit"
-HOMEPAGE="http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=faspftp_runs_v1&m=downloads&s=download_sra"
-SRC_URI="http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-"${PV}".tar.gz"
-# http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sratoolkit.2.0.1-centos_linux64.tar.gz
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static"
-
-DEPEND="app-shells/bash
-	sys-libs/zlib
-	app-arch/bzip2
-	dev-libs/libxml2"
-RDEPEND="${DEPEND}"
-
-# upstream says:
-# icc, icpc are supported: tested with 11.0 (64-bit) and 10.1 (32-bit), 32-bit 11.0 does not work
-
-src_compile(){
-	# # COMP env variable may have 'GCC' or 'ICC' values
-	make OUTDIR="${WORKDIR}"/objdir out || die
-	LIBXML_INCLUDES="/usr/include/libxml2" make dynamic || die
-	LIBXML_INCLUDES="/usr/include/libxml2" make release || die
-	LIBXML_INCLUDES="/usr/include/libxml2" emake || die
-}
-
-src_install(){
-	rm -rf  /var/tmp/portage/sci-biology/"${P}"/image//var
-	# BUG: at the moment every binary is installed three times, e.g.:
-	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump
-	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2
-	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2.1.6
-	if use amd64; then
-		builddir="x86_64"
-	elif use x86; then
-		builddir="i386"
-	fi
-	mkdir "${D}"/usr
-	mkdir "${D}"/usr/bin
-	mkdir -p "${D}"/usr/lib/ncbi
-	mkdir -p "${D}"/usr/ncbi/schema
-	for f in "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*; do cp --preserve=links "$f" "${D}"/usr/bin || die "copy failed" ; done
-	dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*
-
-	# install the main libs and the ncbi/vdb-copy.kfg file
-	insinto /usr/lib/ncbi
-	doins "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/ncbi/*
-
-	insinto /usr/ncbi/schema
-	doins "${W}"/interfaces/align/*.vschema
-	doins "${W}"/interfaces/sra/*.vschema
-	doins "${W}"/interfaces/vdb/*.vschema
-	doins "${W}"/interfaces/ncbi/*.vschema
-	doins "${W}"/interfaces/insdc/*.vschema
-}

diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
deleted file mode 100644
index 02e7e14..0000000
--- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils
-
-W="${WORKDIR}"/"${P}"
-
-DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit"
-HOMEPAGE="http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=faspftp_runs_v1&m=downloads&s=download_sra"
-SRC_URI="http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-"${PV}".tar.gz"
-# http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sratoolkit.2.0.1-centos_linux64.tar.gz
-
-LICENSE="public-domain"
-SLOT="0"
-#KEYWORDS=""
-KEYWORDS="~amd64 ~x86"
-IUSE="static"
-
-DEPEND="app-shells/bash
-	sys-libs/zlib
-	app-arch/bzip2
-	dev-libs/libxml2"
-RDEPEND="${DEPEND}"
-
-# upstream says:
-# icc, icpc are supported: tested with 11.0 (64-bit) and 10.1 (32-bit), 32-bit 11.0 does not work
-
-#src_prepare(){
-	# epatch "${FILESDIR}"/sra_sdk-destdir.patch || die
-	# epatch "${FILESDIR}"/tools_vdb-vcopy_Makefile.patch || die
-	# epatch "${FILESDIR}"/libs_sra_Makefile.patch || die
-	# mkdir -p /var/tmp/portage/sci-biology/"${P}"/image//var/tmp/portage/sci-biology/
-	# ln -s /var/tmp/portage/sci-biology/"${P}" /var/tmp/portage/sci-biology/"${P}"/image//var/tmp/portage/sci-biology/"${P}"
-
-#}
-
-src_compile(){
-	# # COMP env variable may have 'GCC' or 'ICC' values
-	#if use static; then
-	#	emake static LIBDIR=/usr/lib64 DESTDIR="${D}"
-	#else
-	#	emake dynamic LIBDIR=/usr/lib64 DESTDIR="${D}"
-	#fi
-
-	#LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir out LIBDIR=/usr/lib64 DESTDIR="${D}" || die
-	#LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir LIBDIR=/usr/lib64 DESTDIR="${D}" || die
-
-	# preserve the libs written directly into $DESTDIR by ar/ld/gcc
-	#mkdir -p "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/lib
-	#mv "${D}"/usr/lib64/* "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/lib/
-	make OUTDIR="${WORKDIR}"/objdir out || die
-	make dynamic || die
-	make release || die
-	emake || die
-}
-
-src_install(){
-	rm -rf  /var/tmp/portage/sci-biology/"${P}"/image//var
-	# BUG: at the moment every binary is installed three times, e.g.:
-	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump
-	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2
-	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2.1.6
-	if use amd64; then
-		builddir="x86_64"
-	elif use x86; then
-		builddir="i386"
-	fi
-	mkdir "${D}"/usr
-	mkdir "${D}"/usr/bin
-	mkdir -p "${D}"/usr/lib/ncbi
-	mkdir -p "${D}"/usr/ncbi/schema
-
-	# BUG: neither 'doins -r' nor cp --preserve=all work
-	#insinto /usr/bin
-	#doins -r "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*
-	for f in "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*; do cp --preserve=all "$f" "${D}"/usr/bin/ || die "$f copying failed" ; done
-
-	# install the main libs and the ncbi/vdb-copy.kfg file
-	insinto /usr/lib/ncbi
-	doins "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/ncbi/*
-
-	# zap the subdirectory so that copying below does not fail
-	rm -rf "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/ncbi
-
-	# BUG: neither the dolib nor cp --preserve=all work
-	#insinto /usr/lib64
-	#dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*
-	mkdir -p "${D}"/usr/lib64
-	for f in "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*; do cp --preserve=all "$f" "${D}"/usr/lib64/ || die "$f copying failed" ; done
-
-	insinto /usr/ncbi/schema
-	doins "${W}"/interfaces/align/*.vschema
-	doins "${W}"/interfaces/sra/*.vschema
-	doins "${W}"/interfaces/vdb/*.vschema
-	doins "${W}"/interfaces/ncbi/*.vschema
-	doins "${W}"/interfaces/insdc/*.vschema
-}

diff --git a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
index 8719924..d12fbcc 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=4
+EAPI=5
 
 inherit eutils
 
@@ -19,10 +19,11 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="static"
 
-DEPEND="app-shells/bash
+DEPEND="
+	app-shells/bash:*
 	sys-libs/zlib
 	app-arch/bzip2
-	dev-libs/libxml2"
+	dev-libs/libxml2:2="
 RDEPEND="${DEPEND}"
 
 # upstream says:
@@ -51,10 +52,10 @@ src_compile(){
 	# preserve the libs written directly into $DESTDIR by ar/ld/gcc
 	#mkdir -p "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/lib
 	#mv "${D}"/usr/lib64/* "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/lib/
-	make OUTDIR="${WORKDIR}"/objdir out || die
-	make dynamic || die
-	make release || die
-	emake || die
+	emake OUTDIR="${WORKDIR}"/objdir out
+	emake dynamic
+	emake release
+	emake
 }
 
 src_install(){
@@ -68,10 +69,7 @@ src_install(){
 	elif use x86; then
 		builddir="i386"
 	fi
-	mkdir "${D}"/usr
-	mkdir "${D}"/usr/bin
-	mkdir -p "${D}"/usr/lib/ncbi
-	mkdir -p "${D}"/usr/ncbi/schema
+	dodir /usr/bin /usr/lib/ncbi /usr/ncbi/schema
 
 	OBJDIR="${WORKDIR}"/objdir/linux/gcc/dyn/"${builddir}"/rel
 
@@ -82,10 +80,10 @@ src_install(){
 
 	# install the main libs and the ncbi/vdb-copy.kfg file
 	insinto /usr/lib/ncbi
-	doins "${OBJDIR}"/lib/ncbi/*
+	doins "${OBJDIR}"/lib/ncbi/* || die
 
 	# zap the subdirectory so that copying below does not fail
-	rm -rf "${OBJDIR}"/lib/ncbi
+	rm -rf "${OBJDIR}"/lib/ncbi || die
 
 	# BUG: neither the dolib nor cp --preserve=all work
 	#insinto /usr/lib64
@@ -94,9 +92,10 @@ src_install(){
 	for f in "${OBJDIR}"/lib/*; do cp --preserve=all "$f" "${D}"/usr/lib64/ || die "$f copying failed" ; done
 
 	insinto /usr/ncbi/schema
-	doins "${W}"/interfaces/align/*.vschema
-	doins "${W}"/interfaces/sra/*.vschema
-	doins "${W}"/interfaces/vdb/*.vschema
-	doins "${W}"/interfaces/ncbi/*.vschema
-	doins "${W}"/interfaces/insdc/*.vschema
+	doins \
+		"${W}"/interfaces/align/*.vschema \
+		"${W}"/interfaces/sra/*.vschema \
+		"${W}"/interfaces/vdb/*.vschema \
+		"${W}"/interfaces/ncbi/*.vschema \
+		"${W}"/interfaces/insdc/*.vschema
 }