commit: 4261999446148d0a6770f9f6cd73400dff9b1c72
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 08:42:05 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 08:42:31 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=42619994
sci-biology/sra_sdk: fix fetching
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
profiles/package.mask | 1 -
...sra_sdk-2.2.2a.ebuild => sra_sdk-2.10.9.ebuild} | 40 +++-------------------
2 files changed, 5 insertions(+), 36 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 5eb83663f..640ce0789 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -105,4 +105,3 @@ sci-biology/smalt
sci-biology/SnpEff
sci-biology/snphylo
sci-biology/SPAdes
-sci-biology/sra_sdk
diff --git a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
b/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild
similarity index 54%
rename from sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
rename to sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild
index 0c128118d..53e317b5b 100644
--- a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild
+++ b/sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild
@@ -1,22 +1,15 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
-
-inherit eutils
-
-W="${WORKDIR}"/"${P}"
+EAPI=7
DESCRIPTION="NCBI Sequence Read Archive (SRA) sratoolkit"
-HOMEPAGE="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=faspftp_runs_v1&m=downloads&s=download_sra";
-SRC_URI="http://ftp-private.ncbi.nlm.nih.gov/sra/sdk/2.2.2a/sra_sdk-"${PV}".tar.gz";
-#
http://ftp-private.ncbi.nlm.nih.gov/sra/sdk/2.2.2a/sratoolkit.2.2.2a-centos_linux64.tar.gz
+HOMEPAGE="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi
https://github.com/ncbi/sra-tools";
+SRC_URI="https://github.com/ncbi/sra-tools/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="public-domain"
SLOT="0"
-#KEYWORDS=""
-KEYWORDS="~amd64 ~x86"
-IUSE="static"
+KEYWORDS=""
DEPEND="
app-shells/bash:*
@@ -25,32 +18,9 @@ DEPEND="
dev-libs/libxml2:2="
RDEPEND="${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/"${P}"
-
-#}
+S="${WORKDIR}/sra-tools-${PV}"
src_compile(){
- # # COMP env variable may have 'GCC' or 'ICC' values
- #if use static; then
- # emake static LIBDIR=/usr/lib64 DESTDIR="${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/
emake OUTDIR="${WORKDIR}"/objdir out
emake dynamic
emake release
