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

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

commit:     e7df2fee99694eb290f7646148bf8aef3e9f4ac5
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jan  8 12:06:34 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jan  8 12:06:34 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e7df2fee

sci-biology/manatee-igs: new package for prokaryotic genome annotation and editing using chado

---
 sci-biology/manatee-igs/ChangeLog                 |   10 +++
 sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild |   77 +++++++++++++++++++++
 sci-biology/manatee-igs/metadata.xml              |    9 +++
 3 files changed, 96 insertions(+), 0 deletions(-)

diff --git a/sci-biology/manatee-igs/ChangeLog b/sci-biology/manatee-igs/ChangeLog
new file mode 100644
index 0000000..163f6a4
--- /dev/null
+++ b/sci-biology/manatee-igs/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/manatee-igs
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*manatee-igs-2.23.1 (08 Jan 2012)
+
+  08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +manatee-igs-2.23.1.ebuild, +metadata.xml:
+  new package for prokaryotic genome annotation and editing
+

diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
new file mode 100644
index 0000000..b2f4e39
--- /dev/null
+++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="IGS-modified version of the genome annotation tool that can view, modify and store annotation for prokaryotic and eukaryotic genomes."
+HOMEPAGE="http://manatee.sourceforge.net/igs"
+SRC_URI="http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz
+		http://manatee.sourceforge.net/igs/docs/README_Linux.txt"
+
+LICENSE="Artistic-IGS"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="
+		>=dev-libs/expat-1.95.8
+		>=media-libs/gd-2.0.34
+		virtual/perl-CGI
+		dev-perl/DBI
+		dev-perl/DBD-mysql
+		dev-perl/XML-Parser
+		dev-perl/XML-Twig
+		dev-perl/XML-Simple
+		dev-perl/XML-Writer
+		dev-perl/HTML-Template
+		dev-perl/Tree-DAG_Node
+		virtual/perl-File-Spec
+		virtual/perl-Data-Dumper
+		dev-perl/GD
+		dev-perl/GDTextUtil
+		dev-perl/GDGraph
+		virtual/perl-Storable
+		dev-perl/Log-Log4perl
+		dev-perl/Log-Cabin
+		dev-perl/DateManip
+		dev-perl/IO-Tee
+		dev-perl/MLDBM
+		dev-perl/JSON
+		dev-perl/JSON-Any
+		sci-biology/bioperl"
+RDEPEND="${DEPEND}
+		>=dev-db/mysql-5.0
+		>=www-servers/apache-2.2"
+
+S="${WORKDIR}"/manatee-"${PV}"_linux
+
+src_prepare(){
+	find "${S}" -name \*.cgi | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
+	find "${S}" -name \*.pl | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
+	find "${S}" -name \*.pm | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
+}
+
+#src_configure(){
+#	there used to be manateee-="${PV}".tgz file which contained configure script in the past
+#	now the layout is different, temporarily commenting out untill we find the current full sources back again
+#	econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld || die
+#}
+#
+#src_compile(){
+#	emake || die
+#}
+
+src_install(){
+	dodoc ${DISTDIR}"/README_Linux.txt"
+	dodir /var/www/localhost/cgi-bin
+	cp -r src/cgi-bin/chado_prok_manatee "${D}"/var/www/localhost/cgi-bin
+	dodir /var/www/localhost/htdocs/manatee
+	cp -r src/htdocs/tdb "${D}"/var/www/localhost/htdocs/manatee
+
+	einfo "Please read the "${S}"/databases/Makefile.PL and import the databases into your MySQL database"
+
+	einfo "You have to fetch the 1.1 GB large file from http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/lookups-"${PV}"_linux.tgz"
+	einfo "You need to update it regularly."
+	einfo "Also fetch http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/blastdb-"${PV}".tgz (about 2MB in size)"
+}

diff --git a/sci-biology/manatee-igs/metadata.xml b/sci-biology/manatee-igs/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/manatee-igs/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>