commit: d9704bbb3086a2847673b25a93d179f240dc7037
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 15 11:03:39 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jan 15 11:03:39 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d9704bbb
profiles/updates: move sra_sdk to sra-tools
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
profiles/updates/1Q-2022 | 1 +
sci-biology/sra_sdk/files/libs_sra_Makefile.patch | 77 ----------------------
sci-biology/sra_sdk/files/sra_sdk-destdir.patch | 76 ---------------------
.../sra_sdk/files/tools_vdb-vcopy_Makefile.patch | 12 ----
sci-biology/sra_sdk/metadata.xml | 12 ----
sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild | 76 ---------------------
6 files changed, 1 insertion(+), 253 deletions(-)
diff --git a/profiles/updates/1Q-2022 b/profiles/updates/1Q-2022
new file mode 100644
index 000000000..e905430ca
--- /dev/null
+++ b/profiles/updates/1Q-2022
@@ -0,0 +1 @@
+sci-biology/sra_sdk sci-biology/sra-tools
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>[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_sdk/sra_sdk-2.10.9.ebuild
b/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild
deleted file mode 100644
index ef1c8a5d6..000000000
--- a/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-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 -> ${P}.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-# missing dep ngs-sdk
-KEYWORDS=""
-
-DEPEND="
- app-shells/bash:*
- sys-libs/zlib
- app-arch/bzip2
- dev-libs/libxml2:2="
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/sra-tools-${PV}"
-
-src_configure() {
- # this is some non-standard configure script
- ./configure || die
-}
-
-src_compile(){
- 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
-}
