commit: a962286c33cdd407202516174a99befec1a8d8f3 Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Tue Jan 25 13:16:47 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Tue Jan 25 13:16:47 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a962286c
sci-biology/mantee*: drop dead package no update since 2016 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 65 ---------------------- sci-biology/manatee-igs/metadata.xml | 15 ----- sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild | 54 ------------------ sci-biology/manatee-jcvi/metadata.xml | 15 ----- 4 files changed, 149 deletions(-) diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild deleted file mode 100644 index 8a21f8f36..000000000 --- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild +++ /dev/null @@ -1,65 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema" -HOMEPAGE="http://manatee.sourceforge.net/igs"; # no https -SRC_URI="https://downloads.sourceforge.net/project/manatee/igs_manatee/${PV}/manatee-${PV}_linux.tgz"; - -LICENSE="Artistic-Manatee" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - >=dev-libs/expat-1.95.8 - >=media-libs/gd-2.0.34 - dev-perl/CGI - dev-perl/Bio-DB-Das-Chado - 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/Date-Manip - dev-perl/IO-Tee - dev-perl/MLDBM - dev-perl/JSON - dev-perl/JSON-Any - sci-biology/bioperl" -RDEPEND="${DEPEND} - >=virtual/mysql-5:* - >=www-servers/apache-2.2" - -S="${WORKDIR}/manatee-${PV}_linux" - -src_prepare(){ - default - find "${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 $f; done -} - -src_install(){ - dodir /var/www/localhost/cgi-bin - cp -r src/cgi-bin/chado_prok_manatee "${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 https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/lookups-"${PV}"_linux.tgz"; - einfo "You need to update it regularly." - einfo "Also fetch https://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 deleted file mode 100644 index 8a3d26043..000000000 --- a/sci-biology/manatee-igs/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">manatee</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild deleted file mode 100644 index 7bc28decf..000000000 --- a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Genome annotation tool" -HOMEPAGE="http://manatee.sourceforge.net/jcvi/downloads.shtml"; -SRC_URI="http://downloads.sourceforge.net/project/manatee/manatee/manatee-${PV}/manatee-2.4.3.tgz"; - -LICENSE="Artistic-Manatee" -SLOT="0" -KEYWORDS="" - -DEPEND=">=dev-libs/expat-1.95.8 - >=media-libs/gd-2.0.34 - dev-perl/DBI - dev-perl/DBD-mysql - dev-perl/XML-Parser - dev-perl/XML-Twig - dev-perl/XML-Simple - dev-perl/XML-Writer - dev-perl/HTML-Template - dev-perl/Tree-DAG_Node - virtual/perl-File-Spec - virtual/perl-Data-Dumper - dev-perl/GD - virtual/perl-Storable - dev-perl/Log-Log4perl - dev-perl/Log-Cabin - dev-perl/IO-Tee - dev-perl/MLDBM - dev-perl/CGI - dev-perl/DBI - dev-perl/Apache-DBI - dev-perl/Date-Manip -" -# dev-perl/CGI-Carp -# dev-perl/CGI-Cookie -# dev-perl/GD-Text -# dev-perl/GD-Graph -# -RDEPEND="${DEPEND} - >=virtual/mysql-5:* - >=www-servers/apache-2.2" - -S="${WORKDIR}"/manatee-"${PV}" - -src_configure(){ - econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld -} - -src_compile(){ - default -} diff --git a/sci-biology/manatee-jcvi/metadata.xml b/sci-biology/manatee-jcvi/metadata.xml deleted file mode 100644 index 0f267b755..000000000 --- a/sci-biology/manatee-jcvi/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">downloads</remote-id> - </upstream> -</pkgmetadata>
