Initial ebuild

3 files changed, 57 insertions, 0 deletions

diff --git a/sci-biology/pvmsx/Manifest b/sci-biology/pvmsx/Manifest
new file mode 100644
index 000000000..50d661108
--- /dev/null
+++ b/sci-biology/pvmsx/Manifest
@@ -0,0 +1,2 @@
+DIST cdbfasta.tar.gz 59735 SHA256 68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c SHA512 500b3cdf4bf4e21c78a285739c6544e3f2bed377f8e3858c8ace240a9107d765c89cff8004ca2ea001860abc04fc48bc37c03569da5b16115f4419f5fd9bcd5e WHIRLPOOL 3c5beff7ea7d7c6dd6f71755cbb5ea4fabc2ee16aa8d6711906b1a092668cfb889ba56605117133b7e32ab50d6a4986e454f94e32bcd57a5508f1f93788a9dec
+DIST pvmsx.tar.gz 10963 SHA256 c403534a0d13c2457a50c8ff5e9aeb5979d91a56307478b6420b5caf40e62230
diff --git a/sci-biology/pvmsx/metadata.xml b/sci-biology/pvmsx/metadata.xml
new file mode 100644
index 000000000..07b525505
--- /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 000000000..b194f0872
--- /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}
+}