sci-biology/tgi-tools: New ebuild, see http://bugs.gentoo.org/show_bug.cgi?id=157827

svn path=/sunrise/; revision=2279

1 files changed, 44 insertions, 0 deletions

diff --git a/sci-biology/tgi-tools/tgi-tools-0.1.ebuild b/sci-biology/tgi-tools/tgi-tools-0.1.ebuild
new file mode 100644
index 000000000..0471acb20
--- /dev/null
+++ b/sci-biology/tgi-tools/tgi-tools-0.1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+# http://bugs.gentoo.org/show_bug.cgi?id=157827
+
+DESCRIPTION="The Gene Index Project utilities for genomic data processing: seqclean, cdbfasta, psx"
+LICENSE="Artistic"
+HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+for i in seqclean/{seqclean,mdust,trimpoly} cdbfasta/cdbfasta tgicl/{psx,pvmsx,zmsort,tclust,sclust,nrcl,tgi_cpp_library}; do
+	SRC_URI="${SRC_URI} ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/${i}.tar.gz";
+done
+
+RESTRICT="nomirror"
+
+DEPEND=""
+RDEPEND=${DEPEND}
+S=${WORKDIR}
+
+src_unpack() {
+	unpack {seqclean,mdust,trimpoly,cdbfasta,tgi_cpp_library}.tar.gz
+	for i in nrcl sclust tclust zmsort psx pvmsx; do
+		mkdir ${S}/${i}; cd ${S}/${i}; unpack ${i}.tar.gz
+	done
+}
+
+src_compile() {
+	sed -i 's/use Mailer;/#use Mailer;/' ${S}/seqclean/seqclean
+	sed -i 's/-V\t\tverbose/-V\t\tverbose\\/' ${S}/zmsort/zmsort.cpp
+	# TODO: fix errors in nrcl, pvmsx
+	for i in cdbfasta mdust psx sclust tclust trimpoly zmsort; do
+		sed -i 's/CFLAGS[ ]*=/CFLAGS :=/; s/-D_REENTRANT/-D_REENTRANT \${CFLAGS}/; s/CFLAGS[ ]*:=[ ]*-O2$//' ${S}/${i}/Makefile
+		(cd ${S}/${i}; emake) || die
+	done
+}
+
+src_install() {
+	dobin cdbfasta/{cdbfasta,cdbyank} seqclean/{seqclean,cln2qual,bin/seqclean.psx}
+	for i in mdust psx sclust tclust trimpoly zmsort; do dobin ${i}/${i}; done
+}