profiles/updates: move sra_sdk to sra-tools

Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>

7 files changed, 1 insertions, 254 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/Manifest b/sci-biology/sra_sdk/Manifest
deleted file mode 100644
index 336274f86..000000000
--- a/sci-biology/sra_sdk/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST sra_sdk-2.10.9.tar.gz 8788975 BLAKE2B f3d84656f53b1667cc2dcf47f35db3b77723631a143b9af9c2f08b238c8b25ec39825a8ef1043c70fbcc2accf2d60bb79a317f838da33e471bf0d4409fda4bca SHA512 d57a05bf761918bad0c932cd7d3957002333807f7bd756cebd7462716aa941cb8e082cfc6344fb3571dd3fb80d87b4172214fac37d7f0d1bbb198903c97be78c
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-2.10.9.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
-}