commit: a3653f104325e48963deb241fd0a8867e516f76f
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sun Jan 8 23:18:30 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Jan 8 23:18:30 2017 +
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-.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 000..f68a1b6
--- /dev/null
+++ b/sci-biology/vt/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
+sci-biol...@gentoo.org
+Gentoo Biology Project
+
+
diff --git a/sci-biology/vt/vt-.ebuild b/sci-biology/vt/vt-.ebuild
new file mode 100644
index 000..ca197d3
--- /dev/null
+++ b/sci-biology/vt/vt-.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
+}