From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1S2Q1Q-0007vW-IY for garchives@archives.gentoo.org; Tue, 28 Feb 2012 16:35:28 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 1D5B7E0888; Tue, 28 Feb 2012 16:35:21 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id C918AE0888 for ; Tue, 28 Feb 2012 16:35:20 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 91A3B64194 for ; Tue, 28 Feb 2012 16:35:19 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 50601E5400 for ; Tue, 28 Feb 2012 16:35:17 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1330446866.e33c447dad294a8bd8879ddbd308a53c98f8ce40.mmokrejs@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/ChangeLog sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild X-VCS-Directories: sci-biology/sra_sdk/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: e33c447dad294a8bd8879ddbd308a53c98f8ce40 X-VCS-Branch: master Date: Tue, 28 Feb 2012 16:35:17 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: 452afcee-eb7c-4fc1-a525-f4f4f99a1fa7 X-Archives-Hash: 79a7915ac8d1e5a875610c1dca7b1605 commit: e33c447dad294a8bd8879ddbd308a53c98f8ce40 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Tue Feb 28 16:34:26 2012 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Feb 28 16:34:26 2012 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3De33c447d sci-biology/sra_sdk-2.1.9: almost working ebuild (Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit) --- sci-biology/sra_sdk/ChangeLog | 8 +++ sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild | 66 ++++++++++++++++++++++++= +++ sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild | 72 ++++++++++++++++++------= ----- 3 files changed, 119 insertions(+), 27 deletions(-) diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLo= g index 78f9fd1..1a3a884 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: $ =20 +*sra_sdk-2.1.6 (17 Feb 2012) + + 17 Feb 2012; Martin Mokrejs + +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 t= o non- + functional sff-dump + 06 Feb 2012; Martin Mokrejs sra_sdk-2.1.9.ebuild: preserve libs written directly into at the end of src_compile() and in= stall diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild b/sci-biology/sra_s= dk/sra_sdk-2.1.6.ebuild new file mode 100644 index 0000000..83a11e1 --- /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=3D3 + +inherit eutils + +W=3D"${WORKDIR}"/"${P}" + +DESCRIPTION=3D"NCBI Sequence Read Archive (SRA) sratoolkit" +HOMEPAGE=3D"http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=3Dshow&= f=3Dfaspftp_runs_v1&m=3Ddownloads&s=3Ddownload_sra" +SRC_URI=3D"http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-"${PV= }".tar.gz" +# http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sratoolkit.2.0.1-cento= s_linux64.tar.gz + +LICENSE=3D"public-domain" +SLOT=3D"0" +KEYWORDS=3D"~amd64 ~x86" +IUSE=3D"static" + +DEPEND=3D"app-shells/bash + sys-libs/zlib + app-arch/bzip2 + dev-libs/libxml2" +RDEPEND=3D"${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=3D"${WORKDIR}"/objdir out || die + LIBXML_INCLUDES=3D"/usr/include/libxml2" make dynamic || die + LIBXML_INCLUDES=3D"/usr/include/libxml2" make release || die + LIBXML_INCLUDES=3D"/usr/include/libxml2" emake || die +} + +src_install(){ + rm -rf /var/tmp/portage/sci-biology/"${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=3D"x86_64" + elif use x86; then + builddir=3D"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=3Dlinks "$f" "${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 "${W}"/interfaces/insdc/*.vschema +} diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild b/sci-biology/sra_s= dk/sra_sdk-2.1.9.ebuild index ebccf80..703a97f 100644 --- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild +++ b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild @@ -6,6 +6,8 @@ EAPI=3D3 =20 inherit eutils =20 +W=3D"${WORKDIR}"/"${P}" + DESCRIPTION=3D"NCBI Sequence Read Archive (SRA) sratoolkit" HOMEPAGE=3D"http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=3Dshow&= f=3Dfaspftp_runs_v1&m=3Ddownloads&s=3Ddownload_sra" SRC_URI=3D"http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-"${PV= }".tar.gz" @@ -14,7 +16,7 @@ SRC_URI=3D"http://trace.ncbi.nlm.nih.gov/Traces/sra/sta= tic/sra_sdk-"${PV}".tar.gz" LICENSE=3D"public-domain" SLOT=3D"0" #KEYWORDS=3D"" -KEYWORDS=3D"~amd64" +KEYWORDS=3D"~amd64 ~x86" IUSE=3D"static" =20 DEPEND=3D"app-shells/bash @@ -26,29 +28,33 @@ RDEPEND=3D"${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 =20 -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/"${P}"/image//var/tmp/portage/s= ci-biology/ + # ln -s /var/tmp/portage/sci-biology/"${P}" /var/tmp/portage/sci-biolog= y/"${P}"/image//var/tmp/portage/sci-biology/"${P}" =20 -} +#} =20 src_compile(){ - # COMP env variable may have 'GCC' or 'ICC' values - if use static; then - emake static LIBDIR=3D/usr/lib64 DESTDIR=3D"${D}" - else - emake dynamic LIBDIR=3D/usr/lib64 DESTDIR=3D"${D}" - fi + # # COMP env variable may have 'GCC' or 'ICC' values + #if use static; then + # emake static LIBDIR=3D/usr/lib64 DESTDIR=3D"${D}" + #else + # emake dynamic LIBDIR=3D/usr/lib64 DESTDIR=3D"${D}" + #fi =20 - LIBXML_INCLUDES=3D"/usr/include/libxml2" make -j1 OUTDIR=3D"${WORKDIR}"= /objdir out LIBDIR=3D/usr/lib64 DESTDIR=3D"${D}" || die - LIBXML_INCLUDES=3D"/usr/include/libxml2" make -j1 OUTDIR=3D"${WORKDIR}"= /objdir LIBDIR=3D/usr/lib64 DESTDIR=3D"${D}" || die + #LIBXML_INCLUDES=3D"/usr/include/libxml2" make -j1 OUTDIR=3D"${WORKDIR}= "/objdir out LIBDIR=3D/usr/lib64 DESTDIR=3D"${D}" || die + #LIBXML_INCLUDES=3D"/usr/include/libxml2" make -j1 OUTDIR=3D"${WORKDIR}= "/objdir LIBDIR=3D/usr/lib64 DESTDIR=3D"${D}" || die =20 # 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/* "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/lib/ + make OUTDIR=3D"${WORKDIR}"/objdir out || die + make dynamic || die + make release || die + emake || die } =20 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 "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/wmod/* + builddir=3D"x86_64" + elif use x86; then + builddir=3D"i386" fi + mkdir "${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/"${builddir}"/bin/*; do cp -= -preserve=3Dlinks "$f" "${D}"/usr/bin || die "copy failed" ; done + dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/* +=09 + # install the main libs and the ncbi/vdb-copy.kfg file + insinto /usr/lib/ncbi + doins "${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 }