New package sci-biology/consed, bug 253451

(Portage version: 2.2_rc20/cvs/Linux 2.6.26-gentoo-r4 x86_64)

3 files changed, 76 insertions, 0 deletions

diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
new file mode 100644
index 000000000000..3ba58f774c4c
--- /dev/null
+++ b/sci-biology/consed/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/consed
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.1 2009/02/18 16:21:44 weaver Exp $
+
+*consed-19 (18 Feb 2009)
+
+  18 Feb 2009; weaver <weaver@gentoo.org> +metadata.xml, +consed-19.ebuild:
+  New package sci-biology/consed, bug 253451. Ebuild written by Martin Mokrejs
+  <mmokrejs@ribosome.natur.cuni.cz> and me.
+
diff --git a/sci-biology/consed/consed-19.ebuild b/sci-biology/consed/consed-19.ebuild
new file mode 100644
index 000000000000..85e6a7e209e0
--- /dev/null
+++ b/sci-biology/consed/consed-19.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19.ebuild,v 1.1 2009/02/18 16:21:44 weaver Exp $
+
+inherit toolchain-funcs
+
+DESCRIPTION="Consed: a genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="consed-19-sources.tar.gz
+	consed-19-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+DEPEND="x11-libs/openmotif"
+RDEPEND="${DEPEND}
+	>=sci-biology/phrap-1.080721"
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+	einfo "Please visit ${HOMEPAGE} and obtain the file"
+	einfo "\"sources.tar.gz\", then rename it to \"consed-${PV}-sources.tar.gz\""
+	einfo "and place it in ${DISTDIR},"
+	einfo "obtain the file"
+	einfo "\"consed_linux.tar.gz\", then rename it to \"consed-${PV}-linux.tar.gz\""
+	einfo "and place it in ${DISTDIR}"
+}
+
+src_unpack() {
+	unpack ${A}
+	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
+	sed -i -e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \
+		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die
+}
+
+src_compile() {
+	emake || die
+	emake -C misc/mktrace || die
+	emake -C misc/phd2fasta || die
+	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die
+	dobin scripts/* || die
+	insinto /usr/share/${PN}/examples
+	doins -r standard polyphred autofinish assembly_view 454_newbler align454reads align454reads_answer solexa_example solexa_example_answer selectRegions selectRegionsAnswer || die
+	echo 'CONSED_HOME=/usr' > "${S}/99consed"
+	doenvd "${S}/99consed" || die
+	dodoc README.txt *_announcement.txt
+}
diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml
new file mode 100644
index 000000000000..3302123e5718
--- /dev/null
+++ b/sci-biology/consed/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>weaver@gentoo.org</email>
+		<name>Andrey Kislyuk</name>
+	</maintainer>
+	<herd>sci-biology</herd>
+</pkgmetadata>