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

4 files changed, 101 insertions, 0 deletions

diff --git a/sci-biology/manatee-igs/ChangeLog b/sci-biology/manatee-igs/ChangeLog
new file mode 100644
index 000000000..163f6a460
--- /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/Manifest b/sci-biology/manatee-igs/Manifest
new file mode 100644
index 000000000..0b8c52154
--- /dev/null
+++ b/sci-biology/manatee-igs/Manifest
@@ -0,0 +1,5 @@
+DIST README_Linux.txt 9628 RMD160 0a8d8892469ebf2c4b464fdc6074be3b25991959 SHA1 9380f72792ad9c5d272a883f6481294173099138 SHA256 b08bf592d0e81595eba5354e942051e159d3c0a27a8a24a6a78ddc760b4433e3
+DIST manatee-2.23.1_linux.tgz 19879146 RMD160 0bd7e892f20ef91082e48335692548cb757aff27 SHA1 fca80384727ce6683f3b8dcd6a375ad76d4a1530 SHA256 2fca0e6662c2ac56add013a200096d550911dca7ebc83c5932517edad4181533
+EBUILD manatee-igs-2.23.1.ebuild 2602 RMD160 428214a011f3b74bb98748b4e9962e91568b1d83 SHA1 7e245fe2c6fbd7f1cc40645f8cc6678cb31dbade SHA256 1790f305d510bcd3557c8f9e7bbc6cb8eb14254fccea889d65296c27b8c93d63
+MISC ChangeLog 325 RMD160 81449d254b6f5992025cbd737bcb036b89c9781b SHA1 c72ccf329acc82c6da0a00331640e206d485ddfa SHA256 38e7c289301cbf58c89b50af4be45ff44f7e5d8b9baa43f2264338b0df05b650
+MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85
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 000000000..b2f4e39a9
--- /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 000000000..07b525505
--- /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>