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Tue, 22 Sep 2015 08:19:39 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1442908587.a4b81acad6cf95e5d00067340180ff69a07d5a5f.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/sra_sdk/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild X-VCS-Directories: sci-biology/sra_sdk/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: a4b81acad6cf95e5d00067340180ff69a07d5a5f X-VCS-Branch: master Date: Tue, 22 Sep 2015 08:19:39 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 7970857c-82db-4a0a-aa1c-d726ad457acf X-Archives-Hash: 7b1af801b7dd301fdb53f450b3809973 commit: a4b81acad6cf95e5d00067340180ff69a07d5a5f Author: Justin Lecher gentoo org> AuthorDate: Tue Sep 22 07:56:27 2015 +0000 Commit: Justin Lecher gentoo org> CommitDate: Tue Sep 22 07:56:27 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a4b81aca sci-biology/sra_sdk: Bump to EAPI=5 Package-Manager: portage-2.2.21 Signed-off-by: Justin Lecher gentoo.org> sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild | 66 -------------------- sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild | 100 ------------------------------ sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild | 37 ++++++----- 3 files changed, 18 insertions(+), 185 deletions(-) diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild b/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild deleted file mode 100644 index f91cf38..0000000 --- a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild +++ /dev/null @@ -1,66 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -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 deleted file mode 100644 index 02e7e14..0000000 --- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild +++ /dev/null @@ -1,100 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -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://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-"${PV}".tar.gz" -# http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sratoolkit.2.0.1-centos_linux64.tar.gz - -LICENSE="public-domain" -SLOT="0" -#KEYWORDS="" -KEYWORDS="~amd64 ~x86" -IUSE="static" - -DEPEND="app-shells/bash - sys-libs/zlib - app-arch/bzip2 - dev-libs/libxml2" -RDEPEND="${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 - - # BUG: neither 'doins -r' nor cp --preserve=all work - #insinto /usr/bin - #doins -r "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/* - for f in "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*; do cp --preserve=all "$f" "${D}"/usr/bin/ || die "$f copying failed" ; done - - # install the main libs and the ncbi/vdb-copy.kfg file - insinto /usr/lib/ncbi - doins "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/ncbi/* - - # zap the subdirectory so that copying below does not fail - rm -rf "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/ncbi - - # BUG: neither the dolib nor cp --preserve=all work - #insinto /usr/lib64 - #dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/* - mkdir -p "${D}"/usr/lib64 - for f in "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/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 -} diff --git a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild index 8719924..d12fbcc 100644 --- a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild +++ b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ -EAPI=4 +EAPI=5 inherit eutils @@ -19,10 +19,11 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="static" -DEPEND="app-shells/bash +DEPEND=" + app-shells/bash:* sys-libs/zlib app-arch/bzip2 - dev-libs/libxml2" + dev-libs/libxml2:2=" RDEPEND="${DEPEND}" # upstream says: @@ -51,10 +52,10 @@ src_compile(){ # 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="${WORKDIR}"/objdir out || die - make dynamic || die - make release || die - emake || die + emake OUTDIR="${WORKDIR}"/objdir out + emake dynamic + emake release + emake } src_install(){ @@ -68,10 +69,7 @@ src_install(){ 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 + dodir /usr/bin /usr/lib/ncbi /usr/ncbi/schema OBJDIR="${WORKDIR}"/objdir/linux/gcc/dyn/"${builddir}"/rel @@ -82,10 +80,10 @@ src_install(){ # install the main libs and the ncbi/vdb-copy.kfg file insinto /usr/lib/ncbi - doins "${OBJDIR}"/lib/ncbi/* + doins "${OBJDIR}"/lib/ncbi/* || die # zap the subdirectory so that copying below does not fail - rm -rf "${OBJDIR}"/lib/ncbi + rm -rf "${OBJDIR}"/lib/ncbi || die # BUG: neither the dolib nor cp --preserve=all work #insinto /usr/lib64 @@ -94,9 +92,10 @@ src_install(){ 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 "${W}"/interfaces/insdc/*.vschema + doins \ + "${W}"/interfaces/align/*.vschema \ + "${W}"/interfaces/sra/*.vschema \ + "${W}"/interfaces/vdb/*.vschema \ + "${W}"/interfaces/ncbi/*.vschema \ + "${W}"/interfaces/insdc/*.vschema }