commit: d4e2d5a53d73f9a69ca36fbd54fff4ac161398bb Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Thu Apr 30 21:59:43 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Thu Apr 30 21:59:43 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d4e2d5a5
sci-biology/SEECER: added upstream 'patch'; do more proper install process Package-Manager: portage-2.2.18 sci-biology/SEECER/ChangeLog | 7 +++++- sci-biology/SEECER/SEECER-0.1.3-r1.ebuild | 35 ++++++++++++++++++++++++++++++ sci-biology/SEECER/SEECER-0.1.3.ebuild | 34 ----------------------------- sci-biology/SEECER/files/replace_ids.cc | Bin 0 -> 1006 bytes 4 files changed, 41 insertions(+), 35 deletions(-) diff --git a/sci-biology/SEECER/ChangeLog b/sci-biology/SEECER/ChangeLog index 1ac7a38..a57cf30 100644 --- a/sci-biology/SEECER/ChangeLog +++ b/sci-biology/SEECER/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*SEECER-0.1.3-r1 (30 Apr 2015) + + 30 Apr 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> + +SEECER-0.1.3-r1.ebuild, +files/replace_ids.cc, -SEECER-0.1.3.ebuild: + sci-biology/SEECER: added upstream 'patch'; do more proper install process + 10 Jan 2015; Justin Lecher <j...@gentoo.org> SEECER-0.1.3.ebuild: Fix license @@ -10,4 +16,3 @@ 07 Jan 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> +SEECER-0.1.3.ebuild, +metadata.xml: initial ebuild - diff --git a/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild b/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild new file mode 100644 index 0000000..bfebed9 --- /dev/null +++ b/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="SEquencing Error Corrector for RNA-Seq reads" +HOMEPAGE="http://sb.cs.cmu.edu/seecer/"; +SRC_URI=" + http://sb.cs.cmu.edu/seecer/downloads/"${P}".tar.gz + http://sb.cs.cmu.edu/seecer/downloads/manual.pdf -> "${PN}"-manual.pdf" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +# although has bundled jellyfish-1.1.11 copy it just calls the executable during runtime +DEPEND=" + sci-libs/gsl + sci-biology/seqan" +RDEPEND="${DEPEND} + sci-biology/jellyfish" + +S="${S}"/SEECER + +src_prepare(){ + # http://seecer-rna-read-error-correction-mailing-list.21961.x6.nabble.com/Segmentation-fault-in-step-4-td41.html + cp -p "${FILESDIR}"/replace_ids.cc "${S}"/src/ || die +} + +src_install(){ + dobin bin/seecer bin/random_sub_N bin/replace_ids bin/run_jellyfish.sh + dodoc README "${DISTDIR}"/"${PN}"-manual.pdf +} diff --git a/sci-biology/SEECER/SEECER-0.1.3.ebuild b/sci-biology/SEECER/SEECER-0.1.3.ebuild deleted file mode 100644 index d415a01..0000000 --- a/sci-biology/SEECER/SEECER-0.1.3.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -DESCRIPTION="Error corrector for RNA-Seq reads" -HOMEPAGE="http://sb.cs.cmu.edu/seecer/"; -SRC_URI=" - http://sb.cs.cmu.edu/seecer/downloads/SEECER-0.1.3.tar.gz - http://sb.cs.cmu.edu/seecer/downloads/manual.pdf"; - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND=" - sci-libs/gsl - sci-biology/seqan - sci-biology/jellyfish" -RDEPEND="${DEPEND}" - -S="${S}"/SEECER - -# doh, it install /usr/bin/seecer (note the lowercase letters) - -# checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp -# -# Uses: -# libgomp.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/libgomp.so.1 (0x00007f7853faf000) - -# dobin bin/run_seecer.sh -# dodoc "${DISTDIR}"/manual.pdf diff --git a/sci-biology/SEECER/files/replace_ids.cc b/sci-biology/SEECER/files/replace_ids.cc new file mode 100644 index 0000000..0a77819 Binary files /dev/null and b/sci-biology/SEECER/files/replace_ids.cc differ
