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

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

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/*
+}