commit: a3653f104325e48963deb241fd0a8867e516f76f Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Jan 8 23:18:30 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Jan 8 23:18:30 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a3653f10
sci-biology/vt: new package, uses static libs Package-Manager: Portage-2.3.3, Repoman-2.3.1 sci-biology/vt/metadata.xml | 12 ++++++++++ sci-biology/vt/vt-9999.ebuild | 51 +++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 63 insertions(+) diff --git a/sci-biology/vt/metadata.xml b/sci-biology/vt/metadata.xml new file mode 100644 index 0000000..f68a1b6 --- /dev/null +++ b/sci-biology/vt/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/vt/vt-9999.ebuild b/sci-biology/vt/vt-9999.ebuild new file mode 100644 index 0000000..ca197d3 --- /dev/null +++ b/sci-biology/vt/vt-9999.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit git-r3 toolchain-funcs + +DESCRIPTION="A tool set for short variant discovery in genetic sequence data" +HOMEPAGE="https://github.com/atks/vt + http://genome.sph.umich.edu/wiki/vt"; +EGIT_REPO_URI="https://github.com/atks/vt.git"; + +LICENSE="MIT" +SLOT="0" +KEYWORDS="" +IUSE="pdf" + +DEPEND="" +RDEPEND="${DEPEND} + pdf? ( dev-texlive/texlive-latex )" +# >=sci-libs/htslib-1.3.2 +# dev-cpp/tclap +# sci-libs/libsvm +# dev-libs/libpcre +# https://github.com/atks/Rmath + +# The 3rd party stuff is bundled because they have special modifications that +# I made for vt, so it is probably not a good idea to depend on installed components. +# For example TCLAP is modified partially, libsvm has some minor input/output format changes, +# Rmath has the header inclusion to always generate the .a object file + +# Compiles statically bundled version of htslib and Rmath, only libpcre2 is dynamically linked +src_prepare(){ + sed -e "s/= -O3/= ${CFLAGS}/" -i Makefile || die + sed -e 's/^CXX = /CXX ?= /' -i Makefile || die + sed -e "s/-g -Wall -O2/${CFLAGS}/" -i lib/htslib/Makefile || die + sed -e "s/= gcc/= $(tc-getCC)/" -i lib/htslib/Makefile || die + sed -e "s/gcc -g -O3/$(tc-getCC) ${CFLAGS}/" -i lib/pcre2/Makefile || die + sed -e "s/-Wall -O3 -fPIC/${CXXFLAGS} -fPIC/" -i lib/libsvm/Makefile || die +# # TODO zap bundled version of: +# # lib/htslib (version 1.3) +# # lib/tclap +# # lib/Rmath +# # lib/libsvm +# # lib/pcre2 +} + +src_install(){ + dobin vt +}
