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)

3 files changed, 55 insertions, 0 deletions

diff --git a/sci-biology/sra_sdk/Manifest b/sci-biology/sra_sdk/Manifest
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index 000000000..28543c46f
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+++ b/sci-biology/sra_sdk/Manifest
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+DIST sra_sdk-2.0.1.tar.gz 1830293 RMD160 5ee0bbf61484c0afc374bd026792ca7b1f0e99d5 SHA1 cbf5e650c9cd779041a624b3a7e896bf01da1b43 SHA256 6bffbfd21a3e412dce74c26ca579cc9b9a0a66f541ecbce555b2600558f63da4
+EBUILD sra_sdk-2.0.1.ebuild 1398 RMD160 ac1f55041bc140714cc6031a1bde869ae9e419e1 SHA1 d8c96e41eebcc1a925336b46a6ed0e7fffb8d23a SHA256 eea68f0499151975c0c73369558a65d0c736a4b5c2d3edc409a69c72d85a1224
+MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85
diff --git a/sci-biology/sra_sdk/metadata.xml b/sci-biology/sra_sdk/metadata.xml
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+++ b/sci-biology/sra_sdk/metadata.xml
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+<?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 000000000..45d99ca5b
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+++ 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/*
+}