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commit: 4a5df3568fcb228f465287849d51a18cea1bc76a |
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Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Thu Jan 2 08:36:48 2020 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Thu Jan 2 08:36:48 2020 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4a5df356 |
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|
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sci-biology/RAILS: version bump |
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|
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The minimap2-based wrapper script won't work as we do not have minimap2 |
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in Gentoo Linux yet. |
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|
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Package-Manager: Portage-2.3.75, Repoman-2.3.17 |
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Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> |
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|
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.../RAILS/{RAILS-1.4.1.ebuild => RAILS-1.5.1.ebuild} | 14 +++++++++----- |
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1 file changed, 9 insertions(+), 5 deletions(-) |
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|
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diff --git a/sci-biology/RAILS/RAILS-1.4.1.ebuild b/sci-biology/RAILS/RAILS-1.5.1.ebuild |
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similarity index 54% |
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rename from sci-biology/RAILS/RAILS-1.4.1.ebuild |
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rename to sci-biology/RAILS/RAILS-1.5.1.ebuild |
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index 9360c6040..df5f0ea4a 100644 |
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--- a/sci-biology/RAILS/RAILS-1.4.1.ebuild |
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+++ b/sci-biology/RAILS/RAILS-1.5.1.ebuild |
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@@ -1,11 +1,11 @@ |
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-# Copyright 2018 Gentoo Authors |
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+# Copyright 2018-2020 Gentoo Authors |
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# Distributed under the terms of the GNU General Public License v2 |
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|
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EAPI=7 |
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|
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-DESCRIPTION="Cobbler and RAILS scaffolding tools" |
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+DESCRIPTION="Cobbler and RAILS scaffolding tools acting on SAM streams" |
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HOMEPAGE="https://github.com/bcgsc/RAILS" |
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-SRC_URI="https://github.com/bcgsc/RAILS/archive/v1.4.1.tar.gz -> ${P}.tar.gz" |
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+SRC_URI="https://github.com/bcgsc/RAILS/archive/v${PV}.tar.gz -> ${P}.tar.gz" |
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|
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LICENSE="GPL-3+" |
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SLOT="0" |
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@@ -15,12 +15,16 @@ IUSE="" |
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DEPEND="" |
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RDEPEND="${DEPEND} |
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dev-lang/perl |
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- sci-biology/samtools" |
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+ sci-biology/samtools |
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+ sci-biology/bwa |
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+" |
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+# bin/runRAILSminimap.sh calls minimap2 but one can stream the SAM data directly |
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BDEPEND="" |
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|
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src_prepare(){ |
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# remove hardcoded PATHs |
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- sed -e 's@^\.\./@@g' -e 's@^export PATH=/gsc/btl/linuxbrew@#&1@' -i bin/runRAILS.sh || die |
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+ # https://github.com/bcgsc/RAILS/issues/8 |
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+ sed -e 's@^\.\./@@g' -e 's@^export PATH=/gsc/btl/linuxbrew@#&1@' -i bin/*.sh || die |
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default |
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} |
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