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| author |   Justin Lecher <jlec@gentoo.org> | 2017-05-22 07:25:59 +0100 |
|---|---|---|
| committer | Justin Lecher <jlec@gentoo.org> | 2017-05-22 07:28:41 +0100 |
| commit | 78147383c10828c7494fe0979149a1ecb19ded52 (patch) | |
| tree | 1ee01a4e3a649bd730406685dddb300bac21571f | |
| parent | sci-biology/angsd: QA Fixes (diff) | |
| download | sci-78147383c10828c7494fe0979149a1ecb19ded52.tar.gz sci-78147383c10828c7494fe0979149a1ecb19ded52.tar.bz2 sci-78147383c10828c7494fe0979149a1ecb19ded52.zip | |
sci-biology/cortex_var: EAPI bump and QA Fixes
Package-Manager: Portage-2.3.6, Repoman-2.3.2
Signed-off-by: Justin Lecher <jlec@gentoo.org>
| -rw-r--r-- | sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild | 24 | ||||
| -rw-r--r-- | sci-biology/cortex_var/metadata.xml | 2 |
2 files changed, 15 insertions, 11 deletions
diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild index 9d1904062..cfc226ed5 100644 --- a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild +++ b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild @@ -1,14 +1,14 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=6 -PERL_EXPORT_PHASE_FUNCTIONS=no -inherit perl-module eutils toolchain-funcs +inherit perl-functions DESCRIPTION="Genotype variant discovery without reference sequence" HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html" -SRC_URI="http://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v1.0.5.21.tgz +SRC_URI=" + http://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v1.0.5.21.tgz http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf" LICENSE="GPL-3" @@ -18,20 +18,22 @@ IUSE="" # http://www.well.ox.ac.uk/project-stampy -DEPEND="sci-biology/vcftools +DEPEND=" + sci-biology/vcftools sci-libs/gsl - sci-libs/htslib + sci-libs/htslib:0= dev-lang/perl" RDEPEND="${DEPEND}" S="${WORKDIR}"/CORTEX_release_v1.0.5.21 src_prepare(){ + default sed -e "s/ -O3 / ${CFLAGS} /" Makefile || die } src_compile(){ - rm -rf libs/htslib libs/gsl-1.15 + rm -rf libs/htslib libs/gsl-1.15 || die make NUM_COLS=1 MAXK=31 cortex_var || die } @@ -40,7 +42,9 @@ src_install(){ perl_set_version insinto ${VENDOR_LIB} doins scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/* - echo "PATH=/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" > "${S}/99${PN}" - doenvd "${S}/99${PN}" + echo \ + "PATH=/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" \ + > "${T}/99${PN}" || die + doenvd "${T}/99${PN}" dodoc "${DISTDIR}"/cortex_var_user_manual.pdf } diff --git a/sci-biology/cortex_var/metadata.xml b/sci-biology/cortex_var/metadata.xml index fe8a20d2e..aeef1bbec 100644 --- a/sci-biology/cortex_var/metadata.xml +++ b/sci-biology/cortex_var/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> |