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commit: e7df2fee99694eb290f7646148bf8aef3e9f4ac5 |
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Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Sun Jan 8 12:06:34 2012 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Sun Jan 8 12:06:34 2012 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e7df2fee |
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|
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sci-biology/manatee-igs: new package for prokaryotic genome annotation and editing using chado |
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|
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--- |
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sci-biology/manatee-igs/ChangeLog | 10 +++ |
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sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 77 +++++++++++++++++++++ |
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sci-biology/manatee-igs/metadata.xml | 9 +++ |
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3 files changed, 96 insertions(+), 0 deletions(-) |
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|
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diff --git a/sci-biology/manatee-igs/ChangeLog b/sci-biology/manatee-igs/ChangeLog |
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new file mode 100644 |
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index 0000000..163f6a4 |
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--- /dev/null |
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+++ b/sci-biology/manatee-igs/ChangeLog |
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@@ -0,0 +1,10 @@ |
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+# ChangeLog for sci-biology/manatee-igs |
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+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 |
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+# $Header: $ |
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+ |
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+*manatee-igs-2.23.1 (08 Jan 2012) |
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+ |
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+ 08 Jan 2012; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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+ +manatee-igs-2.23.1.ebuild, +metadata.xml: |
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+ new package for prokaryotic genome annotation and editing |
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+ |
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|
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diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild |
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new file mode 100644 |
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index 0000000..b2f4e39 |
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--- /dev/null |
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+++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild |
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@@ -0,0 +1,77 @@ |
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+# Copyright 1999-2012 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Header: $ |
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+ |
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+EAPI=3 |
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+ |
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+DESCRIPTION="IGS-modified version of the genome annotation tool that can view, modify and store annotation for prokaryotic and eukaryotic genomes." |
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+HOMEPAGE="http://manatee.sourceforge.net/igs" |
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+SRC_URI="http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz |
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+ http://manatee.sourceforge.net/igs/docs/README_Linux.txt" |
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+ |
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+LICENSE="Artistic-IGS" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86" |
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+IUSE="" |
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+ |
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+DEPEND=" |
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+ >=dev-libs/expat-1.95.8 |
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+ >=media-libs/gd-2.0.34 |
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+ virtual/perl-CGI |
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+ dev-perl/DBI |
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+ dev-perl/DBD-mysql |
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+ dev-perl/XML-Parser |
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+ dev-perl/XML-Twig |
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+ dev-perl/XML-Simple |
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+ dev-perl/XML-Writer |
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+ dev-perl/HTML-Template |
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+ dev-perl/Tree-DAG_Node |
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+ virtual/perl-File-Spec |
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+ virtual/perl-Data-Dumper |
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+ dev-perl/GD |
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+ dev-perl/GDTextUtil |
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+ dev-perl/GDGraph |
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+ virtual/perl-Storable |
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+ dev-perl/Log-Log4perl |
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+ dev-perl/Log-Cabin |
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+ dev-perl/DateManip |
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+ dev-perl/IO-Tee |
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+ dev-perl/MLDBM |
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+ dev-perl/JSON |
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+ dev-perl/JSON-Any |
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+ sci-biology/bioperl" |
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+RDEPEND="${DEPEND} |
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+ >=dev-db/mysql-5.0 |
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+ >=www-servers/apache-2.2" |
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+ |
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+S="${WORKDIR}"/manatee-"${PV}"_linux |
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+ |
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+src_prepare(){ |
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+ find "${S}" -name \*.cgi | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done |
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+ find "${S}" -name \*.pl | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done |
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+ find "${S}" -name \*.pm | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done |
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+} |
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+ |
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+#src_configure(){ |
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+# there used to be manateee-="${PV}".tgz file which contained configure script in the past |
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+# now the layout is different, temporarily commenting out untill we find the current full sources back again |
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+# econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld || die |
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+#} |
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+# |
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+#src_compile(){ |
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+# emake || die |
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+#} |
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+ |
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+src_install(){ |
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+ dodoc ${DISTDIR}"/README_Linux.txt" |
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+ dodir /var/www/localhost/cgi-bin |
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+ cp -r src/cgi-bin/chado_prok_manatee "${D}"/var/www/localhost/cgi-bin |
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+ dodir /var/www/localhost/htdocs/manatee |
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+ cp -r src/htdocs/tdb "${D}"/var/www/localhost/htdocs/manatee |
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+ |
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+ einfo "Please read the "${S}"/databases/Makefile.PL and import the databases into your MySQL database" |
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+ |
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+ 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" |
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+ einfo "You need to update it regularly." |
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+ einfo "Also fetch http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/blastdb-"${PV}".tgz (about 2MB in size)" |
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+} |
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|
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diff --git a/sci-biology/manatee-igs/metadata.xml b/sci-biology/manatee-igs/metadata.xml |
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new file mode 100644 |
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index 0000000..07b5255 |
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--- /dev/null |
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+++ b/sci-biology/manatee-igs/metadata.xml |
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@@ -0,0 +1,9 @@ |
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+<?xml version="1.0" encoding="UTF-8"?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <herd>sci-biology</herd> |
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+ <maintainer> |
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+ <email>mmokrejs@×××××××××××××××.cz</email> |
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+ <name>Martin Mokrejs</name> |
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+ </maintainer> |
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+</pkgmetadata> |