diff options
Diffstat (limited to 'sci-biology/sra_sdk')
-rw-r--r-- | sci-biology/sra_sdk/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/sra_sdk/files/libs_sra_Makefile.patch | 77 | ||||
-rw-r--r-- | sci-biology/sra_sdk/files/sra_sdk-destdir.patch | 76 | ||||
-rw-r--r-- | sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch | 12 | ||||
-rw-r--r-- | sci-biology/sra_sdk/metadata.xml | 12 | ||||
-rw-r--r-- | sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild | 100 |
6 files changed, 0 insertions, 278 deletions
diff --git a/sci-biology/sra_sdk/Manifest b/sci-biology/sra_sdk/Manifest deleted file mode 100644 index c334775e0..000000000 --- a/sci-biology/sra_sdk/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST sra_sdk-2.2.2a.tar.gz 5105408 BLAKE2B b124251d0172831199697a043f53059f35dcd20757632542a92d10c15dad66ee7ab8b24f55f8a58b0edf81bf93d409db5ef159c93ca5f69cb7b6066802c5eb7d SHA512 748b4892383255da424f50d6757e87e1bea4bc07e2b0dce4ea34fc143b660ad35f06955d75ba439f17223965db93f32f1163118bc68f4fe955c98dd9f5be4c6e diff --git a/sci-biology/sra_sdk/files/libs_sra_Makefile.patch b/sci-biology/sra_sdk/files/libs_sra_Makefile.patch deleted file mode 100644 index 44acc42b0..000000000 --- a/sci-biology/sra_sdk/files/libs_sra_Makefile.patch +++ /dev/null @@ -1,77 +0,0 @@ -diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2011-12-02 21:30:12.000000000 +0100 -+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2012-02-06 18:38:45.000000000 +0100 -@@ -100,7 +100,7 @@ - $(addsuffix .$(LOBX),$(SRAPATH_SRC)) - - $(LIBDIR)/libsrapath.$(LIBX): $(SRAPATH_OBJ) -- $(LD) --slib -o $@ $^ -+ $(LD) --slib -o $(DESTDIR)$@ $^ - - libsrapath.vers.h: - @ true -@@ -138,10 +138,10 @@ - -dklib - - $(LIBDIR)/libsra-schema.$(SHLX): $(SRA_SCHEMA_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRA_SCHEMA_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRA_SCHEMA_LIB) - - $(LIBDIR)/libwsra-schema.$(SHLX): $(WSRA_SCHEMA_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRA_SCHEMA_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRA_SCHEMA_LIB) - - SRASCHEMA_SRC = \ - sraschema-stub -@@ -168,10 +168,10 @@ - $(addsuffix .$(LOBX),$(WSRASCHEMA_SRC)) - - $(LIBDIR)/libsraschema.$(LIBX): $(SRASCHEMA_OBJ) $(SRASCHEMA_DEPS) -- $(LD) --slib -o $@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) -+ $(LD) --slib -o $(DESTDIR)$@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) - - $(LIBDIR)/libwsraschema.$(LIBX): $(WSRASCHEMA_OBJ) $(WSRASCHEMA_DEPS) -- $(LD) --slib -o $@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) -+ $(LD) --slib -o $(DESTDIR)$@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) - - libsraschema_tag: - @ $(TOP)/build/tag-module.sh $(MODULE) libsraschema $(SRASCHEMA_OBJ) -@@ -205,10 +205,10 @@ - -dklib - - $(LIBDIR)/libsradb.$(SHLX): $(SRADB_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) - - $(LIBDIR)/libsradb.$(LIBX): $(SRADB_OBJ) -- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) -+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) - - libsradb_tag: $(SRADB_TAGS) - @ $(TOP)/build/tag-module.sh $(MODULE) libsradb $(SRADB_OBJ) -@@ -236,10 +236,10 @@ - -dklib - - $(LIBDIR)/libwsradb.$(SHLX): $(WSRADB_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) - - $(LIBDIR)/libwsradb.$(LIBX): $(WSRADB_OBJ) -- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) -+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) - - libwsradb_tag: $(WSRADB_TAGS) - @ $(TOP)/build/tag-module.sh $(MODULE) libwsradb $(WSRADB_OBJ) -@@ -266,10 +266,10 @@ - -dklib - - $(LIBDIR)/libsrareader.$(SHLX): $(SRAREADER_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) - - $(LIBDIR)/libsrareader.$(LIBX): $(SRAREADER_OBJ) -- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) -+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) - - libsrareader_tag: - @ $(TOP)/build/tag-module.sh $(MODULE) libsrareader $(SRAREADER_OBJ) diff --git a/sci-biology/sra_sdk/files/sra_sdk-destdir.patch b/sci-biology/sra_sdk/files/sra_sdk-destdir.patch deleted file mode 100644 index bf66c6e46..000000000 --- a/sci-biology/sra_sdk/files/sra_sdk-destdir.patch +++ /dev/null @@ -1,76 +0,0 @@ -diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env 2011-08-31 21:46:21.000000000 +0200 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env 2012-02-06 02:02:38.000000000 +0100 -@@ -141,7 +141,7 @@ - - # create all required output directories - makedirs: -- @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR) -+ @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(DESTDIR)/$(NCBIDIR) - - ifeq (win,$(OS)) - -diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2010-12-28 22:46:39.000000000 +0100 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2012-02-06 02:23:07.000000000 +0100 -@@ -38,10 +38,10 @@ - # versioned output - if [ "$VERS" = "" ] - then -- DLIB_CMD="$DLIB_CMD -o $TARG" -- EXE_CMD="$EXE_CMD -o $TARG" -+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$TARG" -+ EXE_CMD="$EXE_CMD -o $TARG" - else - set-vers $(echo $VERS | tr '.' ' ') -- DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" -- EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS" -+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" -+ EXE_CMD="$EXE_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.$VERS" - fi -diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2010-12-28 22:46:39.000000000 +0100 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2012-02-06 02:34:46.000000000 +0100 -@@ -52,12 +52,12 @@ - - set-vers $(echo $VERS | tr '.' ' ') - --cd "$OUTDIR" || exit 5 -+cd $DESTDIR$OUTDIR || exit 5 - - # create link - create-link () - { -- rm -f "$2" -+ rm -f $DESTDIR"$2" - local CMD="ln -s $1 $2" - echo $CMD - $CMD ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:16.000000000 +0100 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:29.000000000 +0100 -@@ -77,7 +77,7 @@ - CMD="$CMD $TARG" - else - set-vers $(echo $VERS | tr '.' ' ') -- CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS" -+ CMD="$CMD $DESTDIR/$OUTDIR/$NAME$DBGAP.a.$VERS" - fi - - # tack on object files ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc.ori 2012-02-06 04:24:39.000000000 +0100 -+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc 2012-02-06 04:22:57.000000000 +0100 -@@ -36,12 +36,12 @@ - LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \ - --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ - $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) -+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR) - - LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \ - --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ - $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) -+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR) - - # tool options - WARN = -Wall -Wno-variadic-macros # -Wconversion diff --git a/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch b/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch deleted file mode 100644 index 738d67cbd..000000000 --- a/sci-biology/sra_sdk/files/tools_vdb-vcopy_Makefile.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2011-12-02 22:00:36.000000000 +0100 -+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2012-02-06 18:39:05.000000000 +0100 -@@ -89,7 +89,7 @@ - $(BINDIR)/vdb-copy: $(NCBIDIR)/vdb-copy.kfg - - $(NCBIDIR)/vdb-copy.kfg: $(SRCDIR)/vdb-copy.kfg -- cp $^ $@ -+ cp $^ $(DESTDIR)$@ - - VDB_COPY_SRC = \ - num-gen \ diff --git a/sci-biology/sra_sdk/metadata.xml b/sci-biology/sra_sdk/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/sra_sdk/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild deleted file mode 100644 index fd420bf88..000000000 --- a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild +++ /dev/null @@ -1,100 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -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-"${PV}".tar.gz" -# http://ftp-private.ncbi.nlm.nih.gov/sra/sdk/2.2.2a/sratoolkit.2.2.2a-centos_linux64.tar.gz - -LICENSE="public-domain" -SLOT="0" -#KEYWORDS="" -KEYWORDS="~amd64 ~x86" -IUSE="static" - -DEPEND=" - app-shells/bash:* - sys-libs/zlib - app-arch/bzip2 - dev-libs/libxml2:2=" -RDEPEND="${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/ - emake OUTDIR="${WORKDIR}"/objdir out - emake dynamic - emake release - default -} - -src_install(){ - rm -rf /var/tmp/portage/sci-biology/"${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 - dodir /usr/bin /usr/lib/ncbi /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 || die - - # 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 \ - "${W}"/interfaces/sra/*.vschema \ - "${W}"/interfaces/vdb/*.vschema \ - "${W}"/interfaces/ncbi/*.vschema \ - "${W}"/interfaces/insdc/*.vschema -} |