sci-biology/sra_sdk-2.1.9: version bump and almost correct DESTDIR patch

(Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)

5 files changed, 172 insertions, 9 deletions

diff --git a/sci-biology/sra_sdk/ChangeLog b/sci-biology/sra_sdk/ChangeLog
index 994dd9185..0b2163fbf 100644
--- a/sci-biology/sra_sdk/ChangeLog
+++ b/sci-biology/sra_sdk/ChangeLog
@@ -1,7 +1,13 @@
 # ChangeLog for sci-biology/sra_sdk
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*sra_sdk-2.1.9 (06 Feb 2012)
+
+  06 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  sra_sdk-2.1.6.ebuild, +sra_sdk-2.1.9.ebuild, +files/sra_sdk-destdir.patch:
+  version bump and almost correct DESTDIR patch
+
   22 Sep 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   sra_sdk-2.1.6.ebuild:
   adjust to altered source tree strcuture, add weird ncbi/ subdirs to be
diff --git a/sci-biology/sra_sdk/Manifest b/sci-biology/sra_sdk/Manifest
index 9a5abb976..ad6f74df2 100644
--- a/sci-biology/sra_sdk/Manifest
+++ b/sci-biology/sra_sdk/Manifest
@@ -1 +1,2 @@
-DIST sra_sdk-2.1.6.tar.gz 2057465 RMD160 3e5575c5c799cfdc8c0c7edc5d9fd002f1304520 SHA1 b2d1158a2f97484159d0fff53c522b1742bce67b SHA256 c0051287e9c6d00cf059b6ed9e9b922340ae9a75818bc356d47bd5bc33da8e95
+DIST sra_sdk-2.1.6.tar.gz 2057465 SHA256 c0051287e9c6d00cf059b6ed9e9b922340ae9a75818bc356d47bd5bc33da8e95 SHA512 0baa5509b044a5c88313a12205c3d32c9e4036a3a7e5638c26c10d10105104774fa36b4f79907ffb255c7d1eefbd7b22b07d6ab87ab19ed3348e5f3404aff457 WHIRLPOOL 4841ed2b35cf1ddebe57f2878bd5a27e8d314251599869fb7ff159477c3dd107892b8a683e73f9f530bebe5b2a1e4ab0c01743c91813840b12a92f860b18631b
+DIST sra_sdk-2.1.9.tar.gz 4057520 SHA256 ecd417417b34284715a8392c0dc05cd2e3d5e2e32a0ee4ae0db830986456a38e SHA512 b63985a1ea20230b725fcc779eb646f08ec7807c652008dfaa0fd7a6dcead9cab12dd39611e9ae70b5b1dd5aeb0af561894a01e14b1ce341edec75c2915bb030 WHIRLPOOL 62d81fb1ecc68a6c5f9ff1217339461317b30b43cce60d10abc16469ba0ddbeb2e2728fd23133812e6876d37fb06fdf27b2ea0a5dd1932ecbf8c37d626236e9b
diff --git a/sci-biology/sra_sdk/files/sra_sdk-destdir.patch b/sci-biology/sra_sdk/files/sra_sdk-destdir.patch
new file mode 100644
index 000000000..bf66c6e46
--- /dev/null
+++ b/sci-biology/sra_sdk/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_sdk/sra_sdk-2.1.6.ebuild b/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
index 8e964bd81..4e08fb375 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -11,8 +11,8 @@ SRC_URI="http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-"${PV}".tar.gz"
 
 LICENSE="public-domain"
 SLOT="0"
-KEYWORDS=""
-#KEYWORDS="~amd64 ~x86"
+#KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
 IUSE="static"
 
 DEPEND="app-shells/bash
@@ -27,14 +27,14 @@ RDEPEND="${DEPEND}"
 src_compile(){
 	# -I/usr/include/libxml2
 	# -I/var/tmp/portage/sci-biology/sra_sdk-2.0.1/work/sra_sdk-2.0.1/interfaces/os/unix
-	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir out || die
-	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir || die
+	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${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
 
 	# COMP env variable may have 'GCC' or 'ICC' values
 	if use static; then
-		emake static
+		emake static LIBDIR=/usr/lib64 DESTDIR="${D}"
 	else
-		emake dynamic
+		emake dynamic LIBDIR=/usr/lib64 DESTDIR="${D}"
 	fi
 }
 
diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
new file mode 100644
index 000000000..92d51bf2c
--- /dev/null
+++ b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
@@ -0,0 +1,80 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils
+
+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://trace.ncbi.nlm.nih.gov/Traces/sra/static/sra_sdk-"${PV}".tar.gz"
+# http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sratoolkit.2.0.1-centos_linux64.tar.gz
+
+LICENSE="public-domain"
+SLOT="0"
+#KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
+IUSE="static"
+
+DEPEND="app-shells/bash
+	sys-libs/zlib
+	app-arch/bzip2
+	dev-libs/libxml2"
+RDEPEND="${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 "${FILESDIR}"/sra_sdk-destdir.patch || die
+}
+
+src_compile(){
+	# -I/usr/include/libxml2
+	# -I/var/tmp/portage/sci-biology/sra_sdk-2.0.1/work/sra_sdk-2.0.1/interfaces/os/unix
+
+	# COMP env variable may have 'GCC' or 'ICC' values
+	if use static; then
+		emake static LIBDIR=/lib64 DESTDIR="${D}"
+	else
+		emake dynamic LIBDIR=/lib64 DESTDIR="${D}"
+	fi
+
+	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir out LIBDIR=/lib64 DESTDIR="${D}" || die
+	LIBXML_INCLUDES="/usr/include/libxml2" make -j1 OUTDIR="${WORKDIR}"/objdir LIBDIR=/lib64 DESTDIR="${D}" || die
+}
+
+src_install(){
+	# for details see "${WORKDIR}"/sra_sdk-2.1.6/README-build
+
+	# 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
+		dobin "${WORKDIR}"/objdir/linux/pub/gcc/x86_64/bin/*
+		insinto /usr/bin/ncbi
+		dobin "${WORKDIR}"/objdir/linux/pub/gcc/x86_64/bin/ncbi/*
+	elif use x86; then
+		dobin "${WORKDIR}"/objdir/linux/pub/gcc/i386/bin/*
+		insinto /usr/bin/ncbi
+		dobin "${WORKDIR}"/objdir/linux/pub/gcc/i386/bin/ncbi/*
+	fi
+
+	# mkdir -p ${D}/usr/bin || die
+	# for f in ${W}/objdir/linux/rel/gcc/i386/bin/*; do if [ ! -l "$f" ]; then cp "$f" ${D}/usr/bin || die "copy failed" ; fi; done
+
+	# looks the binaries have the folllowing libs statically linked in so we do NOT need these files
+	# mkdir -p ${D}/usr/ilib || die
+	# dolib ${W}/objdir/linux/rel/gcc/i386/ilib/*
+	# insinto "${D}"/usr/lib/ncbi
+	# doins ${W}/objdir/linux/rel/gcc/i386/ilib/ncbi/*
+
+	# mkdir -p ${D}/usr/lib || die
+	# dolib ${W}/objdir/linux/rel/gcc/i386/lib/*
+	# insinto "${D}"/usr/lib/ncbi
+	# doins ${W}/objdir/linux/rel/gcc/i386/lib/ncbi/*
+
+	# same for mod/ and wmod/ subdirs
+}