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| author |   Andrew Ammerlaan <andrewammerlaan@riseup.net> | 2021-01-19 09:42:05 +0100 |
|---|---|---|
| committer | Andrew Ammerlaan <andrewammerlaan@riseup.net> | 2021-01-19 09:42:31 +0100 |
| commit | 4261999446148d0a6770f9f6cd73400dff9b1c72 (patch) | |
| tree | a0553f46683d35df0b7552fe410635a1d2ceff9f | |
| parent | dev-python/persim: version bump to 0.2.0 (diff) | |
| download | sci-4261999446148d0a6770f9f6cd73400dff9b1c72.tar.gz sci-4261999446148d0a6770f9f6cd73400dff9b1c72.tar.bz2 sci-4261999446148d0a6770f9f6cd73400dff9b1c72.zip | |
sci-biology/sra_sdk: fix fetching
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@riseup.net>
| -rw-r--r-- | profiles/package.mask | 1 | ||||
| -rw-r--r-- | sci-biology/sra_sdk/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/sra_sdk/sra_sdk-2.10.9.ebuild (renamed from sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild) | 40 |
3 files changed, 6 insertions, 37 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/Manifest b/sci-biology/sra_sdk/Manifest index c334775e0..336274f86 100644 --- a/sci-biology/sra_sdk/Manifest +++ b/sci-biology/sra_sdk/Manifest @@ -1 +1 @@ -DIST sra_sdk-2.2.2a.tar.gz 5105408 BLAKE2B b124251d0172831199697a043f53059f35dcd20757632542a92d10c15dad66ee7ab8b24f55f8a58b0edf81bf93d409db5ef159c93ca5f69cb7b6066802c5eb7d SHA512 748b4892383255da424f50d6757e87e1bea4bc07e2b0dce4ea34fc143b660ad35f06955d75ba439f17223965db93f32f1163118bc68f4fe955c98dd9f5be4c6e +DIST sra_sdk-2.10.9.tar.gz 8788975 BLAKE2B f3d84656f53b1667cc2dcf47f35db3b77723631a143b9af9c2f08b238c8b25ec39825a8ef1043c70fbcc2accf2d60bb79a317f838da33e471bf0d4409fda4bca SHA512 d57a05bf761918bad0c932cd7d3957002333807f7bd756cebd7462716aa941cb8e082cfc6344fb3571dd3fb80d87b4172214fac37d7f0d1bbb198903c97be78c diff --git a/sci-biology/sra_sdk/sra_sdk-2.2.2a.ebuild b/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 |