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

[Martin Mokrejs]

commit:     e33c447dad294a8bd8879ddbd308a53c98f8ce40
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Feb 28 16:34:26 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 28 16:34:26 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e33c447d

sci-biology/sra_sdk-2.1.9: almost working ebuild

(Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)

---
 sci-biology/sra_sdk/ChangeLog            |    8 +++
 sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild |   66 +++++++++++++++++++++++++++
 sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild |   72 ++++++++++++++++++-----------
 3 files changed, 119 insertions(+), 27 deletions(-)

diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
index 78f9fd1..1a3a884 100644
--- a/sci-biology/sra_sdk/ChangeLog
+++ b/sci-biology/sra_sdk/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*sra_sdk-2.1.6 (17 Feb 2012)
+
+  17 Feb 2012; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  +sra_sdk-2.1.6.ebuild, sra_sdk-2.1.9.ebuild:
+  sci-biology/sra_sdk: updated ebuild for 2.1.6 and 2.1.9: they both
+  compile/install but possibly install layout is still broken, leading to non-
+  functional sff-dump
+
   06 Feb 2012; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
   sra_sdk-2.1.9.ebuild:
   preserve libs written directly into at the end of src_compile() and install

diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild b/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
new file mode 100644
index 0000000..83a11e1
--- /dev/null
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+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
index ebccf80..703a97f 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
@@ -6,6 +6,8 @@ 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-"${PV}".tar.gz"
@@ -14,7 +16,7 @@ SRC_URI="http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-"${PV}".tar.gz"
 LICENSE="public-domain"
 SLOT="0"
 #KEYWORDS=""
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
 IUSE="static"
 
 DEPEND="app-shells/bash
@@ -26,29 +28,33 @@ 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/"${P}"
+#src_prepare(){
+	# epatch "${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
+	# # 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
+	#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/
+	#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(){
@@ -58,14 +64,26 @@ src_install(){
 	# -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
-		mkdir "${D}"/usr
-		mkdir "${D}"/usr/bin
-		dobin "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/bin/*
-		# for f in ${W}/objdir/linux/rel/gcc/i386/bin/*; do if [ ! -l "$f" ]; then cp "$f" ${D}/usr/bin || die "copy failed" ; fi; done
-
-		dolib "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/lib/*
-		dolib "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/ilib/*
-		dolib "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/mod/*
-		dolib "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/wmod/*
+		builddir="x86_64"
+	elif use x86; then
+		builddir="i386"
 	fi
+	mkdir "${D}"/usr
+	mkdir "${D}"/usr/bin
+	mkdir -p "${D}"/usr/lib/ncbi
+	mkdir -p "${D}"/usr/ncbi/schema
+	# dobin "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*
+	for f in "${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
 }