commit: a4b81acad6cf95e5d00067340180ff69a07d5a5f
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 22 07:56:27 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Sep 22 07:56:27 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a4b81aca
sci-biology/sra_sdk: Bump to EAPI=5
Package-Manager: portage-2.2.21
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild | 66 --------------------
sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild | 100 ------------------------------
sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild | 37 ++++++-----
3 files changed, 18 insertions(+), 185 deletions(-)
diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
b/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
deleted file mode 100644
index f91cf38..0000000
--- a/sci-biology/sra_sdk/sra_sdk-2.1.6.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=3
-
-inherit eutils
-
-W="${WORKDIR}"/"${P}"
-
-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-"${PV}".tar.gz";
-#
http://trace.ncbi.nlm.nih.gov/Traces/sra/static/sratoolkit.2.0.1-centos_linux64.tar.gz
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="static"
-
-DEPEND="app-shells/bash
- sys-libs/zlib
- app-arch/bzip2
- dev-libs/libxml2"
-RDEPEND="${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_compile(){
- # # COMP env variable may have 'GCC' or 'ICC' values
- make OUTDIR="${WORKDIR}"/objdir out || die
- LIBXML_INCLUDES="/usr/include/libxml2" make dynamic || die
- LIBXML_INCLUDES="/usr/include/libxml2" make release || die
- LIBXML_INCLUDES="/usr/include/libxml2" emake || die
-}
-
-src_install(){
- rm -rf /var/tmp/portage/sci-biology/"${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
- mkdir "${D}"/usr
- mkdir "${D}"/usr/bin
- mkdir -p "${D}"/usr/lib/ncbi
- mkdir -p "${D}"/usr/ncbi/schema
- for f in "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*; do cp
--preserve=links "$f" "${D}"/usr/bin || die "copy failed" ; done
- dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*
-
- # install the main libs and the ncbi/vdb-copy.kfg file
- insinto /usr/lib/ncbi
- doins "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/ncbi/*
-
- insinto /usr/ncbi/schema
- doins "${W}"/interfaces/align/*.vschema
- doins "${W}"/interfaces/sra/*.vschema
- doins "${W}"/interfaces/vdb/*.vschema
- doins "${W}"/interfaces/ncbi/*.vschema
- doins "${W}"/interfaces/insdc/*.vschema
-}
diff --git a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
b/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
deleted file mode 100644
index 02e7e14..0000000
--- a/sci-biology/sra_sdk/sra_sdk-2.1.9.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-inherit eutils
-
-W="${WORKDIR}"/"${P}"
-
-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 "${FILESDIR}"/sra_sdk-destdir.patch || die
- # epatch "${FILESDIR}"/tools_vdb-vcopy_Makefile.patch || die
- # epatch "${FILESDIR}"/libs_sra_Makefile.patch || die
- # mkdir -p
/var/tmp/portage/sci-biology/"${P}"/image//var/tmp/portage/sci-biology/
- # ln -s /var/tmp/portage/sci-biology/"${P}"
/var/tmp/portage/sci-biology/"${P}"/image//var/tmp/portage/sci-biology/"${P}"
-
-#}
-
-src_compile(){
- # # COMP env variable may have 'GCC' or 'ICC' values
- #if use static; then
- # emake static LIBDIR=/usr/lib64 DESTDIR="${D}"
- #else
- # emake dynamic LIBDIR=/usr/lib64 DESTDIR="${D}"
- #fi
-
- #LIBXML_INCLUDES="/usr/include/libxml2" make -j1
OUTDIR="${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
-
- # preserve the libs written directly into $DESTDIR by ar/ld/gcc
- #mkdir -p "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/lib
- #mv "${D}"/usr/lib64/* "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/lib/
- make OUTDIR="${WORKDIR}"/objdir out || die
- make dynamic || die
- make release || die
- emake || die
-}
-
-src_install(){
- rm -rf /var/tmp/portage/sci-biology/"${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
- mkdir "${D}"/usr
- mkdir "${D}"/usr/bin
- mkdir -p "${D}"/usr/lib/ncbi
- mkdir -p "${D}"/usr/ncbi/schema
-
- # BUG: neither 'doins -r' nor cp --preserve=all work
- #insinto /usr/bin
- #doins -r "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*
- for f in "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/bin/*; do cp
--preserve=all "$f" "${D}"/usr/bin/ || die "$f copying failed" ; done
-
- # install the main libs and the ncbi/vdb-copy.kfg file
- insinto /usr/lib/ncbi
- doins "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/ncbi/*
-
- # zap the subdirectory so that copying below does not fail
- rm -rf "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/ncbi
-
- # BUG: neither the dolib nor cp --preserve=all work
- #insinto /usr/lib64
- #dolib "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*
- mkdir -p "${D}"/usr/lib64
- for f in "${WORKDIR}"/objdir/linux/rel/gcc/"${builddir}"/lib/*; do cp
--preserve=all "$f" "${D}"/usr/lib64/ || die "$f copying failed" ; done
-
- insinto /usr/ncbi/schema
- doins "${W}"/interfaces/align/*.vschema
- doins "${W}"/interfaces/sra/*.vschema
- doins "${W}"/interfaces/vdb/*.vschema
- doins "${W}"/interfaces/ncbi/*.vschema
- doins "${W}"/interfaces/insdc/*.vschema
-}
diff --git a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
index 8719924..d12fbcc 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=4
+EAPI=5
inherit eutils
@@ -19,10 +19,11 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="static"
-DEPEND="app-shells/bash
+DEPEND="
+ app-shells/bash:*
sys-libs/zlib
app-arch/bzip2
- dev-libs/libxml2"
+ dev-libs/libxml2:2="
RDEPEND="${DEPEND}"
# upstream says:
@@ -51,10 +52,10 @@ src_compile(){
# preserve the libs written directly into $DESTDIR by ar/ld/gcc
#mkdir -p "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/lib
#mv "${D}"/usr/lib64/* "${WORKDIR}"/objdir/linux/rel/gcc/x86_64/lib/
- make OUTDIR="${WORKDIR}"/objdir out || die
- make dynamic || die
- make release || die
- emake || die
+ emake OUTDIR="${WORKDIR}"/objdir out
+ emake dynamic
+ emake release
+ emake
}
src_install(){
@@ -68,10 +69,7 @@ src_install(){
elif use x86; then
builddir="i386"
fi
- mkdir "${D}"/usr
- mkdir "${D}"/usr/bin
- mkdir -p "${D}"/usr/lib/ncbi
- mkdir -p "${D}"/usr/ncbi/schema
+ dodir /usr/bin /usr/lib/ncbi /usr/ncbi/schema
OBJDIR="${WORKDIR}"/objdir/linux/gcc/dyn/"${builddir}"/rel
@@ -82,10 +80,10 @@ src_install(){
# install the main libs and the ncbi/vdb-copy.kfg file
insinto /usr/lib/ncbi
- doins "${OBJDIR}"/lib/ncbi/*
+ doins "${OBJDIR}"/lib/ncbi/* || die
# zap the subdirectory so that copying below does not fail
- rm -rf "${OBJDIR}"/lib/ncbi
+ rm -rf "${OBJDIR}"/lib/ncbi || die
# BUG: neither the dolib nor cp --preserve=all work
#insinto /usr/lib64
@@ -94,9 +92,10 @@ src_install(){
for f in "${OBJDIR}"/lib/*; do cp --preserve=all "$f" "${D}"/usr/lib64/
|| die "$f copying failed" ; done
insinto /usr/ncbi/schema
- doins "${W}"/interfaces/align/*.vschema
- doins "${W}"/interfaces/sra/*.vschema
- doins "${W}"/interfaces/vdb/*.vschema
- doins "${W}"/interfaces/ncbi/*.vschema
- doins "${W}"/interfaces/insdc/*.vschema
+ doins \
+ "${W}"/interfaces/align/*.vschema \
+ "${W}"/interfaces/sra/*.vschema \
+ "${W}"/interfaces/vdb/*.vschema \
+ "${W}"/interfaces/ncbi/*.vschema \
+ "${W}"/interfaces/insdc/*.vschema
}
