New package sci-biology/consed, bug 253451

Package-Manager: portage-2.2_rc20/cvs/Linux 2.6.26-gentoo-r4 x86_64

4 files changed, 81 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/Manifest b/sci-biology/consed/Manifest
new file mode 100644
index 000000000000..b3f01946d69e
--- /dev/null
+++ b/sci-biology/consed/Manifest
@@ -0,0 +1,5 @@
+DIST consed-19-linux.tar.gz 29835559 RMD160 06765fe4beee2bb8f1f72b7cb9522acadf8df1d3 SHA1 7b01affde92cda6ff0bcb49199ed6c7e60b044d5 SHA256 27501d714e4cd7ea04def6a7f985b674bc454ed8bd7d1e86b41b0283e2b9e089
+DIST consed-19-sources.tar.gz 6867357 RMD160 52bb03197a75827214b30c8ce833d9479fc9aa63 SHA1 ee40c48b887fc457c869b0d997ca650a0a7864af SHA256 1db37b17608e49470926dae261c76d400cf3f9eb5feea52cd732e0bfa4cadee3
+EBUILD consed-19.ebuild 1798 RMD160 e4e94ae5197232f70743e0d3818e7b55ca6bd83a SHA1 596ef69ecec6ca631fba6b6f8d4605f3dcf1f565 SHA256 e334fea21b68680a55b6b61da6e1b80cb9005616fc7551fe36616a3a2387ed3c
+MISC ChangeLog 435 RMD160 08ac7abec8febb64edbb4f4f8112d7413b5cb7c9 SHA1 ea9e5f68264b09f73a3a85695bee4e63c9b60f0a SHA256 0e90f68c90e1d454f4c1843ec0fda9fac132932960894543c6125dfb39cfef66
+MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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>