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author | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2012-02-28 17:34:26 +0100 |
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committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2012-02-28 17:34:26 +0100 |
commit | e33c447dad294a8bd8879ddbd308a53c98f8ce40 (patch) | |
tree | 5ec697118a8da5d2f963732925fd8314ef52b9e9 /sci-biology | |
parent | sci-biology/gbrowse-2.48: added dependency on <=sci-biology/primer3-2, per ht... (diff) | |
download | sci-e33c447dad294a8bd8879ddbd308a53c98f8ce40.tar.gz sci-e33c447dad294a8bd8879ddbd308a53c98f8ce40.tar.bz2 sci-e33c447dad294a8bd8879ddbd308a53c98f8ce40.zip |
sci-biology/sra_sdk-2.1.9: almost working ebuild
(Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/sra_sdk/ChangeLog | 8 | ||||
-rw-r--r-- | sci-biology/sra_sdk/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild | 66 | ||||
-rw-r--r-- | sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild | 72 |
4 files changed, 120 insertions, 27 deletions
diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog index 78f9fd11b..1a3a88468 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/Manifest b/sci-biology/sra_sdk/Manifest index 53acb93cb..ad6f74df2 100644 --- a/sci-biology/sra_sdk/Manifest +++ b/sci-biology/sra_sdk/Manifest @@ -1 +1,2 @@ +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 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 000000000..83a11e1a7 --- /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 "${W}"/interfaces/insdc/*.vschema +} diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild index ebccf807a..703a97fd1 100644 --- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild +++ b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild @@ -6,6 +6,8 @@ EAPI=3 inherit eutils +W="${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 } |