commit: a7af360682db36d643bb33a18e550f7fc15fbbd7 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Sat Jan 15 11:02:23 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Sat Jan 15 11:02:23 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a7af3606
sci-biology/sra-tools: rename from sra_sdk, add version 2,11,3 Closes: https://github.com/gentoo/sci/issues/982 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> .../sra-tools/files/libs_sra_Makefile.patch | 77 ++++++++++++++++++++++ sci-biology/sra-tools/files/sra_sdk-destdir.patch | 76 +++++++++++++++++++++ .../sra-tools/files/tools_vdb-vcopy_Makefile.patch | 12 ++++ sci-biology/sra-tools/metadata.xml | 12 ++++ sci-biology/sra-tools/sra-tools-2.11.3.ebuild | 48 ++++++++++++++ 5 files changed, 225 insertions(+) diff --git a/sci-biology/sra-tools/files/libs_sra_Makefile.patch b/sci-biology/sra-tools/files/libs_sra_Makefile.patch new file mode 100644 index 000000000..44acc42b0 --- /dev/null +++ b/sci-biology/sra-tools/files/libs_sra_Makefile.patch @@ -0,0 +1,77 @@ +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-tools/files/sra_sdk-destdir.patch b/sci-biology/sra-tools/files/sra_sdk-destdir.patch new file mode 100644 index 000000000..bf66c6e46 --- /dev/null +++ b/sci-biology/sra-tools/files/sra_sdk-destdir.patch @@ -0,0 +1,76 @@ +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-tools/files/tools_vdb-vcopy_Makefile.patch b/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch new file mode 100644 index 000000000..738d67cbd --- /dev/null +++ b/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch @@ -0,0 +1,12 @@ +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-tools/metadata.xml b/sci-biology/sra-tools/metadata.xml new file mode 100644 index 000000000..138cb7705 --- /dev/null +++ b/sci-biology/sra-tools/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>[email protected]</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/sra-tools/sra-tools-2.11.3.ebuild b/sci-biology/sra-tools/sra-tools-2.11.3.ebuild new file mode 100644 index 000000000..57c5b881e --- /dev/null +++ b/sci-biology/sra-tools/sra-tools-2.11.3.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit" +HOMEPAGE="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi https://github.com/ncbi/sra-tools"; +SRC_URI="https://github.com/ncbi/sra-tools/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="public-domain" +SLOT="0" +# Fix ncbi-vdb first +KEYWORDS="" + +DEPEND=" + sys-libs/zlib + app-arch/bzip2 + dev-libs/libxml2:2= + sci-libs/hdf5 + sci-biology/ngs + sci-biology/ncbi-vdb +" + +RDEPEND="${DEPEND}" + +S="${WORKDIR}/sra-tools-${PV}" + +src_configure() { + # this is some non-standard configure script + ./configure \ + --with-ngs-sdk-prefix=/usr/ngs/ngs-sdk \ + --with-hdf5-prefix=/usr \ + || die +} + +src_install() { + dodir /usr/include + dodir /etc/profile.d + # Hard way around hard coded paths + find . -type f -exec sed -i \ + -e "s:/usr/local:${ED}/usr:g" \ + -e "s:/etc:${ED}/etc:g" \ + -e "s:/usr/lib:${ED}/usr/lib:g" \ + -e "s:/usr/include:${ED}/usr/include:g" \ + -e "s:setup.py -q install:setup.py install --root="${D}":g" \ + {} \; || die + default +}
