diff options
Diffstat (limited to 'sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild')
| -rw-r--r-- | sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild | 72 |
1 files changed, 45 insertions, 27 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 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 } |