* [gentoo-commits] proj/sci:master commit in: sci-biology/sra-tools/, sci-biology/sra-tools/files/
@ 2022-01-15 11:04 Andrew Ammerlaan
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From: Andrew Ammerlaan @ 2022-01-15 11:04 UTC (permalink / raw
To: gentoo-commits
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>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-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
+}
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