commit: 1747e93926b4fc0e704589b65ce0f4701941e673 Author: Jonas Maaskola <jonas <AT> maaskola <DOT> de> AuthorDate: Sat Nov 29 16:04:36 2014 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Mon Dec 1 15:24:41 2014 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1747e939
Add discrover ebuilds --- sci-biology/discrover/discrover-1.1.2.ebuild | 74 ++++++++++++++++++++++++++++ sci-biology/discrover/discrover-9999.ebuild | 74 ++++++++++++++++++++++++++++ sci-biology/discrover/metadata.xml | 22 +++++++++ 3 files changed, 170 insertions(+) diff --git a/sci-biology/discrover/discrover-1.1.2.ebuild b/sci-biology/discrover/discrover-1.1.2.ebuild new file mode 100644 index 0000000..f1cac2a --- /dev/null +++ b/sci-biology/discrover/discrover-1.1.2.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 +inherit cmake-utils + +DESCRIPTION="A sequence motif discovery tool that uses discriminative learning" +HOMEPAGE="https://github.com/maaskola/discrover"; +SRC_URI="https://github.com/maaskola/discrover/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="dreme doc +logo misc_scripts +rmathlib tcmalloc" + +RDEPEND=" + dev-libs/boost + dreme? ( sci-biology/meme ) + logo? ( + dev-lang/ruby + dev-texlive/texlive-latex + dev-tex/pgf + dev-tex/xcolor + media-gfx/imagemagick + ) + misc_scripts? ( dev-lang/ruby ) + rmathlib? ( dev-lang/R ) + tcmalloc? ( dev-util/google-perftools ) +" +DEPEND="${RDEPEND} + doc? ( + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + dev-texlive/texlive-latexrecommended + media-gfx/imagemagick + ) +" +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_with dreme DREME) + $(cmake-utils_use_with doc DOC) + $(cmake-utils_use_with logo LOGO) + $(cmake-utils_use_with misc_scripts MISC_SCRIPTS) + $(cmake-utils_use_with rmathlib RMATHLIB) + $(cmake-utils_use_with tcmalloc TCMALLOC) + ) + + unset R_HOME + + if use rmathlib ; then + elog + elog "Using statistical routines from standalone Rmathlib." + elog + fi + if use dreme ; then + elog + elog "Linking to DREME from the MEME suite." + elog + else + elog + elog "Not linking to DREME from the MEME suite (sci-biology/meme)." + elog "You will not be able to use DREME to find seeds." + elog + fi + + if use doc ; then + elog + elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf" + elog + fi + + cmake-utils_src_configure +} diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild new file mode 100644 index 0000000..1d0ac53 --- /dev/null +++ b/sci-biology/discrover/discrover-9999.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 +inherit cmake-utils git-2 + +DESCRIPTION="A sequence motif discovery tool that uses discriminative learning" +HOMEPAGE="https://github.com/maaskola/discrover"; +EGIT_REPO_URI="https://github.com/maaskola/${PN}"; + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="dreme doc +logo misc_scripts +rmathlib tcmalloc" + +RDEPEND=" + dev-libs/boost + dreme? ( sci-biology/meme ) + logo? ( + dev-lang/ruby + dev-texlive/texlive-latex + dev-tex/pgf + dev-tex/xcolor + media-gfx/imagemagick + ) + misc_scripts? ( dev-lang/ruby ) + rmathlib? ( dev-lang/R ) + tcmalloc? ( dev-util/google-perftools ) +" +DEPEND="${RDEPEND} + doc? ( + dev-texlive/texlive-latex + dev-texlive/texlive-latexextra + dev-texlive/texlive-latexrecommended + media-gfx/imagemagick + ) +" +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_with dreme DREME) + $(cmake-utils_use_with doc DOC) + $(cmake-utils_use_with logo LOGO) + $(cmake-utils_use_with misc_scripts MISC_SCRIPTS) + $(cmake-utils_use_with rmathlib RMATHLIB) + $(cmake-utils_use_with tcmalloc TCMALLOC) + ) + + unset R_HOME + + if use rmathlib ; then + elog + elog "Using statistical routines from standalone Rmathlib." + elog + fi + if use dreme ; then + elog + elog "Linking to DREME from the MEME suite." + elog + else + elog + elog "Not linking to DREME from the MEME suite (sci-biology/meme)." + elog "You will not be able to use DREME to find seeds." + elog + fi + + if use doc ; then + elog + elog "User manual available at /usr/share/doc/discrover/discrover-manual.pdf" + elog + fi + + cmake-utils_src_configure +} diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml new file mode 100644 index 0000000..cda9ddd --- /dev/null +++ b/sci-biology/discrover/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer> + <email>jo...@maaskola.de</email> + <name>Jonas Maaskola</name> + </maintainer> + <use> + <flag name="dreme"> + Allow to use DREME from the MEME package for seeding + </flag> + <flag name="logo"> + Enable LaTeX/TikZ based ruby script for sequence logo drawing + </flag> + <flag name="misc_scripts"> + Install miscellaneous scripts, e.g. for sequence length statistics + </flag> + <flag name="rmathlib"> + Link to the standalone Rmathlib for statistical routines + </flag> + </use> +</pkgmetadata>
