commit: c1d81c6bb160f87609eb3005d0ac9457649aeda2 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon May 15 23:27:17 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon May 15 23:27:17 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c1d81c6b
sci-biology/MaSuRCA: version bump The package is actually a bundle of many, including SOAPdenovo2 somewhat patched so that it compiles (unlike vanilla 2.04-r240). Package-Manager: Portage-2.3.5, Repoman-2.3.2 sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild | 57 ------------------------------- sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild | 34 ++++++++++++++++++ 2 files changed, 34 insertions(+), 57 deletions(-) diff --git a/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild b/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild deleted file mode 100644 index 38a3d703e..000000000 --- a/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -DESCRIPTION="Assembler to combine Sanger, Roche 454 and Illumina Solexa reads" -HOMEPAGE="http://www.genome.umd.edu/masurca.html"; -SRC_URI="ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA-"${PV}".tar.gz - ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"; - -LICENSE="BSD GPL-2 GPL-3" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND="dev-lang/perl - app-arch/bzip2" -RDEPEND="${DEPEND} - >=sci-biology/quorum-0.2.1 - >=sci-biology/jellyfish-1.1.11" - -# the ebuild mimics "${S}"/install.sh -src_configure(){ - cd jellyfish || die - econf - - cd ../CA/kmer || die - econf - - cd ../../SuperReads || die - econf - - cd ../quorum || die - econf --enable-relative-paths --with-relative-jf-path -} - -src_compile(){ - cd jellyfish || die - default - - cd ../CA/kmer || die - default - - cd ../../CA/src || die - default - - cd ../SuperReads || die - default - - cd ../quorum || die - default -} - -src_install(){ - dobin masurca - dodoc sr_config_example.txt -} diff --git a/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild b/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild new file mode 100644 index 000000000..d9e667792 --- /dev/null +++ b/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore" +HOMEPAGE="http://www.genome.umd.edu/masurca.html"; +SRC_URI="${P}.tar.gz + ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"; + +LICENSE="BSD GPL-2 GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=">=dev-lang/perl-5.8 + app-arch/bzip2" +RDEPEND="${DEPEND}" + +RESTRICT="fetch" + +# the ebuild mimics "${S}"/install.sh +src_configure(){ + ./install.sh || die +} + +src_compile(){ + ./install.sh || die +} + +src_install(){ + dobin masurca + dodoc sr_config_example.txt +}
