commit: a064c41bd0283321afe151af6a49e83873bade3f Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon May 18 22:01:27 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon May 18 22:01:27 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a064c41b
sci-biology/breakdancer: upstream moved to github Package-Manager: portage-2.2.18 sci-biology/breakdancer/ChangeLog | 8 ++++- sci-biology/breakdancer/breakdancer-1.1.2.ebuild | 20 ------------ sci-biology/breakdancer/breakdancer-9999.ebuild | 40 ++++++++++++++++++++++++ 3 files changed, 47 insertions(+), 21 deletions(-) diff --git a/sci-biology/breakdancer/ChangeLog b/sci-biology/breakdancer/ChangeLog index 2dfc569..1fbaee5 100644 --- a/sci-biology/breakdancer/ChangeLog +++ b/sci-biology/breakdancer/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-biology/breakdancer -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*breakdancer-9999 (18 May 2015) + + 18 May 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> + +breakdancer-9999.ebuild, -Manifest, -breakdancer-1.1.2.ebuild: + sci-biology/breakdancer: upstream moved to github + *breakdancer-1.1.2 (23 Mar 2014) 23 Mar 2014; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> diff --git a/sci-biology/breakdancer/breakdancer-1.1.2.ebuild b/sci-biology/breakdancer/breakdancer-1.1.2.ebuild deleted file mode 100644 index 6aff868..0000000 --- a/sci-biology/breakdancer/breakdancer-1.1.2.ebuild +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -DESCRIPTION="Genome-wide detection of structural variants from next generation paired-end sequencing reads" -HOMEPAGE="http://breakdancer.sourceforge.net"; -SRC_URI="http://sourceforge.net/projects/breakdancer/files/breakdancer-1.1.2_2013_03_08.zip"; - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND="dev-lang/perl - dev-perl/Statistics-Descriptive - dev-perl/Math-CDF - sci-biology/samtools" -RDEPEND="${DEPEND}" diff --git a/sci-biology/breakdancer/breakdancer-9999.ebuild b/sci-biology/breakdancer/breakdancer-9999.ebuild new file mode 100644 index 0000000..11888b4 --- /dev/null +++ b/sci-biology/breakdancer/breakdancer-9999.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +[ "$PV" == "9999" ] && inherit git-r3 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="Genome-wide detection of structural variants from next generation paired-end sequencing reads" +HOMEPAGE="http://breakdancer.sourceforge.net"; +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/genome/breakdancer.git"; + KEYWORDS="" +else + # TODO: fish out 1.3.6 version from github + SRC_URI="http://sourceforge.net/projects/breakdancer/files/breakdancer-1.1.2_2013_03_08.zip"; + KEYWORDS="" +fi + +LICENSE="GPL-3" +SLOT="0" +IUSE="" + +# http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm +DEPEND="dev-lang/perl + dev-perl/Statistics-Descriptive + sci-biology/samtools" +RDEPEND="${DEPEND}" + +# cd breakdancer +# mkdir build +# cd build +# cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local +# ... +# -- Build files have been written to: .../breakdancer/build +# make +# make install
