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

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* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2011-06-10 15:37 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2011-06-10 15:37 UTC (permalink / raw
  To: gentoo-commits

commit:     1764e30dd8d96ceb1afdb045bf6468a1ffb7440b
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jun 10 15:37:28 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jun 10 15:37:28 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1764e30d

sci-biology/sra_sdk-2.0.1: quote properly

(Portage version: 2.1.9.49/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild b/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild
index 68b2336..f8708e1 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild
@@ -30,9 +30,9 @@ src_compile(){
 
 src_install(){
 	if use amd64; then
-		dobin ${WORKDIR}"/objdir/linux/rel/gcc/x86_64/bin/*"
+		dobin "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/bin/*
 	elif use x86; then
-		dobin ${WORKDIR}"/objdir/linux/rel/gcc/i386/bin/*"
+		dobin "${WORKDIR}"/objdir/linux/rel/gcc/i386/bin/*
 	fi
 
 	# mkdir -p ${D}/usr/bin || die



^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2021-02-04  5:42 Andrew Ammerlaan
  0 siblings, 0 replies; 17+ messages in thread
From: Andrew Ammerlaan @ 2021-02-04  5:42 UTC (permalink / raw
  To: gentoo-commits

commit:     a9ad84affbf5a38c4e689c715731f16d5bb199f6
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Feb  4 05:42:50 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Feb  4 05:42:50 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a9ad84af

sci-biology/sra_sdk: call configure correctly for this pack

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild b/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild
index 53e317b5b..ef1c8a5d6 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild
@@ -9,6 +9,7 @@ SRC_URI="https://github.com/ncbi/sra-tools/archive/${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="public-domain"
 SLOT="0"
+# missing dep ngs-sdk
 KEYWORDS=""
 
 DEPEND="
@@ -20,6 +21,11 @@ RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/sra-tools-${PV}"
 
+src_configure() {
+	# this is some non-standard configure script
+	./configure || die
+}
+
 src_compile(){
 	emake OUTDIR="${WORKDIR}"/objdir out
 	emake dynamic


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2021-01-13 21:06 Andrew Ammerlaan
  0 siblings, 0 replies; 17+ messages in thread
From: Andrew Ammerlaan @ 2021-01-13 21:06 UTC (permalink / raw
  To: gentoo-commits

commit:     4091f595d6b8f6c1f44ae7899e1487de50fca10d
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Jan 13 21:05:52 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Jan 13 21:05:52 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4091f595

sci-biology/sra_sdk: use https for homepage

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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 fd420bf88..0c128118d 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -8,7 +8,7 @@ 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"
+HOMEPAGE="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=faspftp_runs_v1&m=downloads&s=download_sra"
 SRC_URI="http://ftp-private.ncbi.nlm.nih.gov/sra/sdk/2.2.2a/sra_sdk-"${PV}".tar.gz"
 # http://ftp-private.ncbi.nlm.nih.gov/sra/sdk/2.2.2a/sratoolkit.2.2.2a-centos_linux64.tar.gz
 


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2015-09-22  8:19 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2015-09-22  8:19 UTC (permalink / raw
  To: gentoo-commits

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
 }


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2013-03-03 17:52 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2013-03-03 17:52 UTC (permalink / raw
  To: gentoo-commits

commit:     036b7eed303dc8e864a0e5f51dfc10e64231da79
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar  3 16:23:32 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar  3 16:23:32 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=036b7eed

sci-biology/sra_sdk: Drop useless blank line

Package-Manager: portage-2.2.0_alpha164

---
 sci-biology/sra_sdk/ChangeLog             |    6 +++++-
 sci-biology/sra_sdk/metadata.xml          |   10 +++++-----
 sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild  |    6 +-----
 sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild |    6 +-----
 4 files changed, 12 insertions(+), 16 deletions(-)

diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
index a57b683..38b6c28 100644
--- a/sci-biology/sra_sdk/ChangeLog
+++ b/sci-biology/sra_sdk/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/sra_sdk
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  03 Mar 2013; Justin Lecher <jlec@gentoo.org> sra_sdk-2.1.9.ebuild,
+  sra_sdk-2.2.2a.ebuild, metadata.xml:
+  Drop useless blank line
+
 *sra_sdk-2.2.2a (28 Dec 2012)
 
   28 Dec 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/sra_sdk/metadata.xml b/sci-biology/sra_sdk/metadata.xml
index 07b5255..2bc8930 100644
--- a/sci-biology/sra_sdk/metadata.xml
+++ b/sci-biology/sra_sdk/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-biology</herd>
-	<maintainer>
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>

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 bfbb577..db79050 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -78,8 +78,6 @@ src_install(){
 	#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/*
@@ -87,8 +85,6 @@ src_install(){
 	# 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/*

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 c759f57..dee4cde 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -80,8 +80,6 @@ src_install(){
 	#doins -r "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*
 	for f in "${OBJDIR}"/bin/*; do cp --preserve=all "$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 "${OBJDIR}"/lib/ncbi/*
@@ -89,8 +87,6 @@ src_install(){
 	# zap the subdirectory so that copying below does not fail
 	rm -rf "${OBJDIR}"/lib/ncbi
 
-
-
 	# BUG: neither the dolib nor cp --preserve=all work
 	#insinto /usr/lib64
 	#dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2012-12-28 19:19 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2012-12-28 19:19 UTC (permalink / raw
  To: gentoo-commits

commit:     a62460750fb06d27ecfffb78dc3f1f34bb3321d7
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec 28 19:11:40 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec 28 19:11:40 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a6246075

sci-biology/sra_sdk-2.2.2a: a version bump, still requires MAKEOPTS=-j1 and copies softlinks to binaries and libraries as files, so everything is in 3 physical copies

Package-Manager: portage-2.1.11.38

---
 sci-biology/sra_sdk/ChangeLog             |    9 ++-
 sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild |  106 +++++++++++++++++++++++++++++
 2 files changed, 114 insertions(+), 1 deletions(-)

diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
index 6965e3d..a57b683 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-2.2.2a (28 Dec 2012)
+
+  28 Dec 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +sra_sdk-2.2.2a.ebuild:
+  sci-biology/sra_sdk-2.2.2a: a version bump, still requires MAKEOPTS=-j1 and
+  copies softlinks to binaries and libraries as files, so everything is in 3
+  physical copies
+
   15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   sra_sdk-2.1.9.ebuild:
   added missing insinto sra_sdk-2.1.9.ebuild
@@ -53,4 +61,3 @@
   sra_sdk-2.0.1.ebuild:
   backbone of a new package, should probably use a lot of stuff from
   ncbi-tools++ ebuild
-

diff --git a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
new file mode 100644
index 0000000..c759f57
--- /dev/null
+++ b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
@@ -0,0 +1,106 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+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://ftp-private.ncbi.nlm.nih.gov/sra/sdk/2.2.2a/sra_sdk-"${PV}".tar.gz"
+# http://ftp-private.ncbi.nlm.nih.gov/sra/sdk/2.2.2a/sratoolkit.2.2.2a-centos_linux64.tar.gz
+
+LICENSE="public-domain"
+SLOT="0"
+#KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
+IUSE="static"
+
+DEPEND="app-shells/bash
+	sys-libs/zlib
+	app-arch/bzip2
+	dev-libs/libxml2"
+RDEPEND="${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
+
+	OBJDIR="${WORKDIR}"/objdir/linux/gcc/dyn/"${builddir}"/rel
+
+	# BUG: neither 'doins -r' nor cp --preserve=all work
+	#insinto /usr/bin
+	#doins -r "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*
+	for f in "${OBJDIR}"/bin/*; do cp --preserve=all "$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 "${OBJDIR}"/lib/ncbi/*
+
+	# zap the subdirectory so that copying below does not fail
+	rm -rf "${OBJDIR}"/lib/ncbi
+
+
+
+	# BUG: neither the dolib nor cp --preserve=all work
+	#insinto /usr/lib64
+	#dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*
+	mkdir -p "${D}"/usr/lib64
+	for f in "${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
+}


^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2012-03-15 22:58 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2012-03-15 22:58 UTC (permalink / raw
  To: gentoo-commits

commit:     bd09c6bedf15fec7a2bc06a3596e4e53570f8e35
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 15 22:57:48 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 15 22:57:48 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bd09c6be

sci-biology/sra_sdk-2.1.9: added missing insinto

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

---
 sci-biology/sra_sdk/ChangeLog            |    4 ++++
 sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild |    1 +
 2 files changed, 5 insertions(+), 0 deletions(-)

diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
index 9b86b3a..6965e3d 100644
--- a/sci-biology/sra_sdk/ChangeLog
+++ b/sci-biology/sra_sdk/ChangeLog
@@ -4,6 +4,10 @@
 
   15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   sra_sdk-2.1.9.ebuild:
+  added missing insinto sra_sdk-2.1.9.ebuild
+
+  15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  sra_sdk-2.1.9.ebuild:
   use EAPI=4 hoping it will handle symlinks in bin/ and lib/ directories
   properly (but it does not, bug #408199 sra_sdk-2.1.9.ebuild
 

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 6baa61c..bfbb577 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
@@ -90,6 +90,7 @@ src_install(){
 
 
 	# 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



^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2012-03-15 21:23 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2012-03-15 21:23 UTC (permalink / raw
  To: gentoo-commits

commit:     129e2c6e82a71b4ae4894081ce2384f302f2d096
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 15 21:22:57 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 15 21:22:57 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=129e2c6e

sci-biology/sra_sdk-2.1.9: use EAPI=4 hoping it will handle symlinks in bin/ and lib/ directories properly (but it does not, bug #408199

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

---
 sci-biology/sra_sdk/ChangeLog            |    5 +++++
 sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild |   22 ++++++++++++++++++----
 2 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
index 1a3a884..9b86b3a 100644
--- a/sci-biology/sra_sdk/ChangeLog
+++ b/sci-biology/sra_sdk/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  sra_sdk-2.1.9.ebuild:
+  use EAPI=4 hoping it will handle symlinks in bin/ and lib/ directories
+  properly (but it does not, bug #408199 sra_sdk-2.1.9.ebuild
+
 *sra_sdk-2.1.6 (17 Feb 2012)
 
   17 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

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 cf9c639..6baa61c 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=4
 
 inherit eutils
 
@@ -72,14 +72,28 @@ src_install(){
 	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/"${builddir}"/lib/*
+
+	# BUG: neither 'doins -r' nor cp --preserve=all work
+	#insinto /usr/bin
+	#doins -r "${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
+	#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



^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2012-02-28 16:36 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2012-02-28 16:36 UTC (permalink / raw
  To: gentoo-commits

commit:     ca80860f99c79fe10300b6400338d1cb7e8681af
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Feb 28 16:36:27 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 28 16:36:27 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ca80860f

sci-biology/sra_sdk-2.1.9: remove trailing whitespace

---
 sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

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 703a97f..cf9c639 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
@@ -75,7 +75,7 @@ src_install(){
 	# 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/*



^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2012-02-28 16:35 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2012-02-28 16:35 UTC (permalink / raw
  To: gentoo-commits

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@fold.natur.cuni.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@fold.natur.cuni.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
 }



^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2012-02-06 18:56 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2012-02-06 18:56 UTC (permalink / raw
  To: gentoo-commits

commit:     644e4b2c3b32a18745448407c5c705a53ee09d9f
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Feb  6 18:55:58 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb  6 18:55:58 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=644e4b2c

sci-biology-sra_sdk-2.1.9: preserve libs written directly into  at the end of src_compile() and install them later on

(Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)

---
 sci-biology/sra_sdk/ChangeLog            |    5 +++++
 sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild |   13 +++++++++----
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
index 9ac722a..78f9fd1 100644
--- a/sci-biology/sra_sdk/ChangeLog
+++ b/sci-biology/sra_sdk/ChangeLog
@@ -3,6 +3,11 @@
 # $Header: $
 
   06 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  sra_sdk-2.1.9.ebuild:
+  preserve libs written directly into at the end of src_compile() and install
+  them later on sra_sdk-2.1.9.ebuild
+
+  06 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   sra_sdk-2.1.9.ebuild, +files/libs_sra_Makefile.patch,
   +files/tools_vdb-vcopy_Makefile.patch:
   two more Makefiles needed a DESTDIR patch, in conjunction with an ugly

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 fcc74cb..ebccf80 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
@@ -38,13 +38,17 @@ src_prepare(){
 src_compile(){
 	# COMP env variable may have 'GCC' or 'ICC' values
 	if use static; then
-		emake static LIBDIR=/lib64 DESTDIR="${D}"
+		emake static LIBDIR=/usr/lib64 DESTDIR="${D}"
 	else
-		emake dynamic LIBDIR=/lib64 DESTDIR="${D}"
+		emake dynamic LIBDIR=/usr/lib64 DESTDIR="${D}"
 	fi
 
-	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir out LIBDIR=/lib64 DESTDIR="${D}" || die
-	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir LIBDIR=/lib64 DESTDIR="${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/
 }
 
 src_install(){
@@ -59,6 +63,7 @@ src_install(){
 		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/*



^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2012-02-06 18:26 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2012-02-06 18:26 UTC (permalink / raw
  To: gentoo-commits

commit:     7916128a6fb3f84c3c63e2c99dbe2e3e4d93d2e8
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Feb  6 18:26:13 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Feb  6 18:26:13 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7916128a

sci-biology/sra_sdk-2.1.6: dropping an old crap

---
 sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild |   73 ------------------------------
 1 files changed, 0 insertions(+), 73 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 4e08fb3..0000000
--- a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-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_compile(){
-	# -I/usr/include/libxml2
-	# -I/var/tmp/portage/sci-biology/sra_sdk-2.0.1/work/sra_sdk-2.0.1/interfaces/os/unix
-	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
-
-	# 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
-}
-
-src_install(){
-	# for details see "${WORKDIR}"/sra_sdk-2.1.6/README-build
-
-	# BUG: at the moment every binary is installed three times, e.g.:
-	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump
-	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2
-	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2.1.6
-	if use amd64; then
-		dobin "${WORKDIR}"/objdir/linux/pub/gcc/x86_64/bin/*
-		insinto /usr/bin/ncbi
-		dobin "${WORKDIR}"/objdir/linux/pub/gcc/x86_64/bin/ncbi/*
-	elif use x86; then
-		dobin "${WORKDIR}"/objdir/linux/pub/gcc/i386/bin/*
-		insinto /usr/bin/ncbi
-		dobin "${WORKDIR}"/objdir/linux/pub/gcc/i386/bin/ncbi/*
-	fi
-
-	# mkdir -p ${D}/usr/bin || die
-	# 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
-
-	# looks the binaries have the folllowing libs statically linked in so we do NOT need these files
-	# mkdir -p ${D}/usr/ilib || die
-	# dolib ${W}/objdir/linux/rel/gcc/i386/ilib/*
-	# insinto "${D}"/usr/lib/ncbi
-	# doins ${W}/objdir/linux/rel/gcc/i386/ilib/ncbi/*
-
-	# mkdir -p ${D}/usr/lib || die
-	# dolib ${W}/objdir/linux/rel/gcc/i386/lib/*
-	# insinto "${D}"/usr/lib/ncbi
-	# doins ${W}/objdir/linux/rel/gcc/i386/lib/ncbi/*
-
-	# same for mod/ and wmod/ subdirs
-}



^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2011-09-22 23:35 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2011-09-22 23:35 UTC (permalink / raw
  To: gentoo-commits

commit:     56a8bd4198774a33f0883a4cbcad0366e76e3473
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Sep 22 23:35:41 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Sep 22 23:35:41 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=56a8bd41

sci-biology/sra_sdk-2.1.6: adjust to altered source tree strcuture, add weird ncbi/ subdirs to be installed, more comments in the ebuild

(Portage version: 2.1.10.19/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/sra_sdk/ChangeLog            |    5 ++++
 sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild |   31 ++++++++++++++++++++++++++---
 2 files changed, 32 insertions(+), 4 deletions(-)

diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
index b1c199c..994dd91 100644
--- a/sci-biology/sra_sdk/ChangeLog
+++ b/sci-biology/sra_sdk/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  22 Sep 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  sra_sdk-2.1.6.ebuild:
+  adjust to altered source tree strcuture, add weird ncbi/ subdirs to be
+  installed, more comments in the ebuild
+
 *sra_sdk-2.1.6 (22 Sep 2011)
 
   22 Sep 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>

diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild b/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
index 86aee29..8e964bd 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
@@ -13,7 +13,7 @@ LICENSE="public-domain"
 SLOT="0"
 KEYWORDS=""
 #KEYWORDS="~amd64 ~x86"
-IUSE=""
+IUSE="static"
 
 DEPEND="app-shells/bash
 	sys-libs/zlib
@@ -29,22 +29,45 @@ src_compile(){
 	# -I/var/tmp/portage/sci-biology/sra_sdk-2.0.1/work/sra_sdk-2.0.1/interfaces/os/unix
 	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir out || die
 	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir || die
+
+	# COMP env variable may have 'GCC' or 'ICC' values
+	if use static; then
+		emake static
+	else
+		emake dynamic
+	fi
 }
 
 src_install(){
+	# for details see "${WORKDIR}"/sra_sdk-2.1.6/README-build
+
+	# BUG: at the moment every binary is installed three times, e.g.:
+	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump
+	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2
+	# -rwxr-xr-x 1 root root 1797720 Sep 23 01:31 abi-dump.2.1.6
 	if use amd64; then
-		dobin "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/bin/*
+		dobin "${WORKDIR}"/objdir/linux/pub/gcc/x86_64/bin/*
+		insinto /usr/bin/ncbi
+		dobin "${WORKDIR}"/objdir/linux/pub/gcc/x86_64/bin/ncbi/*
 	elif use x86; then
-		dobin "${WORKDIR}"/objdir/linux/rel/gcc/i386/bin/*
+		dobin "${WORKDIR}"/objdir/linux/pub/gcc/i386/bin/*
+		insinto /usr/bin/ncbi
+		dobin "${WORKDIR}"/objdir/linux/pub/gcc/i386/bin/ncbi/*
 	fi
 
 	# mkdir -p ${D}/usr/bin || die
 	# 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
 
-	# looks the binaries have the folllowing libs statically linked
+	# looks the binaries have the folllowing libs statically linked in so we do NOT need these files
 	# mkdir -p ${D}/usr/ilib || die
 	# dolib ${W}/objdir/linux/rel/gcc/i386/ilib/*
+	# insinto "${D}"/usr/lib/ncbi
+	# doins ${W}/objdir/linux/rel/gcc/i386/ilib/ncbi/*
 
 	# mkdir -p ${D}/usr/lib || die
 	# dolib ${W}/objdir/linux/rel/gcc/i386/lib/*
+	# insinto "${D}"/usr/lib/ncbi
+	# doins ${W}/objdir/linux/rel/gcc/i386/lib/ncbi/*
+
+	# same for mod/ and wmod/ subdirs
 }



^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2011-09-22 21:34 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2011-09-22 21:34 UTC (permalink / raw
  To: gentoo-commits

commit:     e25a0e68f4df4fac8a12cee21b5e255efe01067b
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Sep 22 21:33:57 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Sep 22 21:33:57 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e25a0e68

sci-biology/sra_sdk-2.1.6: version bump

(Portage version: 2.1.10.19/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/sra_sdk/ChangeLog                      |    6 ++++++
 .../{sra_sdk-2.0.1.ebuild => sra_sdk-2.1.6.ebuild} |    1 +
 2 files changed, 7 insertions(+), 0 deletions(-)

diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
index 67fd8f4..b1c199c 100644
--- a/sci-biology/sra_sdk/ChangeLog
+++ b/sci-biology/sra_sdk/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*sra_sdk-2.1.6 (22 Sep 2011)
+
+  22 Sep 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  -sra_sdk-2.0.1.ebuild, +sra_sdk-2.1.6.ebuild:
+  version bump sra_sdk-2.1.6.ebuild
+
   30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   sra_sdk-2.0.1.ebuild:
   backbone of a new package, should probably use a lot of stuff from

diff --git a/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild b/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
similarity index 98%
rename from sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild
rename to sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
index 5777c88..86aee29 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
@@ -21,6 +21,7 @@ DEPEND="app-shells/bash
 	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(){



^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2011-07-30 11:08 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2011-07-30 11:08 UTC (permalink / raw
  To: gentoo-commits

commit:     9e635549c3410a82e9252685738217870dcf5879
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jul 30 11:08:04 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jul 30 11:08:04 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9e635549

backbone of a new package, should probably use a lot of stuff from ncbi-tools++ ebuild

(Portage version: 2.1.10.7/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/sra_sdk/ChangeLog            |    9 +++++++++
 sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild |    4 +++-
 2 files changed, 12 insertions(+), 1 deletions(-)

diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
new file mode 100644
index 0000000..67fd8f4
--- /dev/null
+++ b/sci-biology/sra_sdk/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/sra_sdk
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  sra_sdk-2.0.1.ebuild:
+  backbone of a new package, should probably use a lot of stuff from
+  ncbi-tools++ ebuild
+

diff --git a/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild b/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild
index f8708e1..5777c88 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild
@@ -7,10 +7,12 @@ EAPI=3
 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"
+KEYWORDS=""
+#KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 DEPEND="app-shells/bash



^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2011-06-10 15:30 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2011-06-10 15:30 UTC (permalink / raw
  To: gentoo-commits

commit:     113e78501cc56feaeb6be9bed99ca631505c1b41
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jun 10 15:30:43 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jun 10 15:30:43 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=113e7850

sci-biology/sra_sdk-2.0.1: fix install for amd64

(Portage version: 2.1.9.49/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild |    6 +++++-
 1 files changed, 5 insertions(+), 1 deletions(-)

diff --git a/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild b/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild
index 45d99ca..68b2336 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild
@@ -29,7 +29,11 @@ src_compile(){
 }
 
 src_install(){
-	dobin ${WORKDIR}"/objdir/linux/rel/gcc/i386/bin/*"
+	if use amd64; then
+		dobin ${WORKDIR}"/objdir/linux/rel/gcc/x86_64/bin/*"
+	elif use x86; then
+		dobin ${WORKDIR}"/objdir/linux/rel/gcc/i386/bin/*"
+	fi
 
 	# mkdir -p ${D}/usr/bin || die
 	# 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



^ permalink raw reply related	[flat|nested] 17+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/
@ 2011-06-10 15:23 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2011-06-10 15:23 UTC (permalink / raw
  To: gentoo-commits

commit:     b0206f3c92333456a460c81f033a467391ebd6f2
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jun 10 15:23:04 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jun 10 15:23:04 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b0206f3c

sci-biology/sra_sdk-2.0.1: a new package to access NCBI Short Read Archive

(Portage version: 2.1.9.49/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/sra_sdk/metadata.xml         |    9 ++++++
 sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild |   43 ++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+), 0 deletions(-)

diff --git a/sci-biology/sra_sdk/metadata.xml b/sci-biology/sra_sdk/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/sra_sdk/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<maintainer>
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+</pkgmetadata>

diff --git a/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild b/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild
new file mode 100644
index 0000000..45d99ca
--- /dev/null
+++ b/sci-biology/sra_sdk/sra_sdk-2.0.1.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+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-"${PV}".tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="app-shells/bash
+	sys-libs/zlib
+	app-arch/bzip2
+	dev-libs/libxml2"
+RDEPEND="${DEPEND}"
+
+# icc, icpc are supported: tested with 11.0 (64-bit) and 10.1 (32-bit), 32-bit 11.0 does not work
+
+src_compile(){
+	# -I/usr/include/libxml2
+	# -I/var/tmp/portage/sci-biology/sra_sdk-2.0.1/work/sra_sdk-2.0.1/interfaces/os/unix
+	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir out || die
+	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir || die
+}
+
+src_install(){
+	dobin ${WORKDIR}"/objdir/linux/rel/gcc/i386/bin/*"
+
+	# mkdir -p ${D}/usr/bin || die
+	# 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
+
+	# looks the binaries have the folllowing libs statically linked
+	# mkdir -p ${D}/usr/ilib || die
+	# dolib ${W}/objdir/linux/rel/gcc/i386/ilib/*
+
+	# mkdir -p ${D}/usr/lib || die
+	# dolib ${W}/objdir/linux/rel/gcc/i386/lib/*
+}



^ permalink raw reply related	[flat|nested] 17+ messages in thread

end of thread, other threads:[~2021-02-04  5:42 UTC | newest]

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