diff options
author | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2012-12-28 20:11:40 +0100 |
---|---|---|
committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2012-12-28 20:11:40 +0100 |
commit | a62460750fb06d27ecfffb78dc3f1f34bb3321d7 (patch) | |
tree | cbaad95f4ef9e73cedeb925e11c254ea2a55dc91 /sci-biology/sra_sdk | |
parent | added for testing (diff) | |
download | sci-a62460750fb06d27ecfffb78dc3f1f34bb3321d7.tar.gz sci-a62460750fb06d27ecfffb78dc3f1f34bb3321d7.tar.bz2 sci-a62460750fb06d27ecfffb78dc3f1f34bb3321d7.zip |
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
Diffstat (limited to 'sci-biology/sra_sdk')
-rw-r--r-- | sci-biology/sra_sdk/ChangeLog | 9 | ||||
-rw-r--r-- | sci-biology/sra_sdk/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild | 106 |
3 files changed, 115 insertions, 1 deletions
diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog index 6965e3d02..a57b68364 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/Manifest b/sci-biology/sra_sdk/Manifest index ad6f74df2..68882f1e5 100644 --- a/sci-biology/sra_sdk/Manifest +++ b/sci-biology/sra_sdk/Manifest @@ -1,2 +1,3 @@ DIST sra_sdk-2.1.6.tar.gz 2057465 SHA256 c0051287e9c6d00cf059b6ed9e9b922340ae9a75818bc356d47bd5bc33da8e95 SHA512 0baa5509b044a5c88313a12205c3d32c9e4036a3a7e5638c26c10d10105104774fa36b4f79907ffb255c7d1eefbd7b22b07d6ab87ab19ed3348e5f3404aff457 WHIRLPOOL 4841ed2b35cf1ddebe57f2878bd5a27e8d314251599869fb7ff159477c3dd107892b8a683e73f9f530bebe5b2a1e4ab0c01743c91813840b12a92f860b18631b DIST sra_sdk-2.1.9.tar.gz 4057520 SHA256 ecd417417b34284715a8392c0dc05cd2e3d5e2e32a0ee4ae0db830986456a38e SHA512 b63985a1ea20230b725fcc779eb646f08ec7807c652008dfaa0fd7a6dcead9cab12dd39611e9ae70b5b1dd5aeb0af561894a01e14b1ce341edec75c2915bb030 WHIRLPOOL 62d81fb1ecc68a6c5f9ff1217339461317b30b43cce60d10abc16469ba0ddbeb2e2728fd23133812e6876d37fb06fdf27b2ea0a5dd1932ecbf8c37d626236e9b +DIST sra_sdk-2.2.2a.tar.gz 5105408 SHA256 c5fc85c435e86325f4c2d2124c790121a6c22168958faee3fa0a59fe47d7f120 SHA512 748b4892383255da424f50d6757e87e1bea4bc07e2b0dce4ea34fc143b660ad35f06955d75ba439f17223965db93f32f1163118bc68f4fe955c98dd9f5be4c6e WHIRLPOOL 19c971b21a0771e6cc013f9f41977294c63ee62f1be643efdf553e97d16468e2c3d96692cbc506a42549d1835d0d1272306e44682c680890b7a479d11101fecd 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 000000000..c759f57b6 --- /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 +} |