[gentoo-commits] proj/sci:master commit in: sci-biology/pvmsx/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     3010ecf4051cb4cbab7d5adfceca5bccf1e312df
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan  7 22:11:27 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan  7 22:11:27 2015 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3010ecf4

Initial ebuild

---
 sci-biology/pvmsx/metadata.xml     |  9 ++++++++
 sci-biology/pvmsx/pvmsx-0.1.ebuild | 46 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 55 insertions(+)

diff --git a/sci-biology/pvmsx/metadata.xml b/sci-biology/pvmsx/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/pvmsx/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<maintainer>
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+</pkgmetadata>

diff --git a/sci-biology/pvmsx/pvmsx-0.1.ebuild b/sci-biology/pvmsx/pvmsx-0.1.ebuild
new file mode 100644
index 0000000..b194f08
--- /dev/null
+++ b/sci-biology/pvmsx/pvmsx-0.1.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="parallel multi-FASTA file processing tool using PVM from TIGR Gene Indices project tools, an alternative to psx"
+HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
+SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz
+		ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/cdbfasta.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="sys-cluster/pvm"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}
+
+src_unpack(){
+	mkdir ${PN} || die
+	cd ${PN} || die "Failed to chdir"
+	unpack ${PN}.tar.gz || die
+}
+
+src_prepare() {
+	# we need gclib from cdbfasta.tar.gz bundle which has fewer files than tgi_cpp_library.tar.gz wbut has e.g. GStr.h
+	sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' "${S}"/${PN}/Makefile || die "Failed to run sed"
+	sed -i 's#GCLDIR := ../gclib#GCLDIR := ../cdbfasta/gclib#' "${S}"/"${PN}"/Makefile || die
+	sed -i "s#-I-#-iquote#" ${S}/${PN}/Makefile
+	cd ${PN} || die
+	ln -s ../cdbfasta/gcl . || die "Cannot make a softlink"
+}
+
+src_compile() {
+	cd ${PN} || die
+	emake || die "emake failed in "${S}"/${PN}"
+}
+
+src_install() {
+	cd ${PN} || die
+	dobin ${PN} || die "Failed to install ${PN} binary"
+	newdoc README README.${PN}
+}