[gentoo-commits] proj/sci:master commit in: profiles/, sci-biology/cg-cat/

[Andrew Ammerlaan]

commit:     7274db93040bd4ab606516086f295add64e1107d
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 31 09:18:51 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Aug 31 09:18:51 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7274db93

sci-biology/cg-cat: remove last-rited pack

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 profiles/package.mask                     |  1 -
 sci-biology/cg-cat/cg-cat-20150130.ebuild | 59 -------------------------------
 sci-biology/cg-cat/metadata.xml           | 12 -------
 3 files changed, 72 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index 8916d3ac2..a58bd71ee 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -37,7 +37,6 @@
 # Bug #798015, removal in 30 days.
 # Perhaps these packages work with the newer ncbi-tools++? If anyone is actively
 # using these packages please open a bug report
-sci-biology/cg-cat
 sci-biology/cgview-bin
 sci-biology/prot4EST
 sci-biology/seqclean

diff --git a/sci-biology/cg-cat/cg-cat-20150130.ebuild b/sci-biology/cg-cat/cg-cat-20150130.ebuild
deleted file mode 100644
index 0c48ecbc5..000000000
--- a/sci-biology/cg-cat/cg-cat-20150130.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="r2cat and treecat, scaffolding tools for ordering and orienting contigs"
-HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/cgcat"
-SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/downloads/r2cat.tar.gz"
-# SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/downloads/r2cat.jar"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="${DEPEND}
-	>=virtual/jre-1.6:*
-	dev-lang/perl
-	sci-biology/ncbi-tools"
-DEPEND="${RDEPEND}
-	>=virtual/jdk-1.6:*
-	dev-java/ant-core"
-
-S="${WORKDIR}"/r2cat
-
-src_prepare(){
-	default
-	sed -e "s#/vol/bioapps#"${D}"/usr#" -e "s#/vol/bibidev/r2cat#"${D}"/usr#" -i Makefile || die
-	sed -e "s#/vol/gnu#/usr#" -i de/bielefeld/uni/cebitec/r2cat/blast_to_r2cat.pl || die
-}
-
-src_compile(){
-	emake r2cat.jar
-}
-
-src_install(){
-	# emake install dies with:
-	# jarsigner -tsa https://timestamp.geotrust.com/tsa -keystore /homes/phuseman/.gnupg/jarsigner_keystore_cg-cat  cg-cat.jar cgcat
-	# Enter Passphrase for keystore: jarsigner: you must enter key password
-	# Makefile:44: recipe for target 'cg-cat.jar' failed
-	mkdir -p "${D}"/usr/share/r2cat
-	# emake install_cebitec
-	# emake install_bibiserv
-	# the blast_to_r2cat.pl script needs bioperl
-	dobin de/bielefeld/uni/cebitec/r2cat/blast_to_r2cat.pl
-	java-pkg_dojar r2cat.jar || die
-	dodoc README.md ReadmeLicenses.txt
-	docinto html
-	dodoc de/bielefeld/uni/cebitec/r2cat/help/*
-}
-
-# to start r2cat:
-# java -Xmx10240M -jar r2cat.jar de.bielefeld.uni.cebitec.r2cat.R2cat
-
-# to start treecat:
-# java -Xmx10240M -cp r2cat.jar de.bielefeld.uni.cebitec.treecat.Treecat -Xmx -d64
-
-# add -d64 on the java commandline if you need more than 4GB of memory and your system can handle it

diff --git a/sci-biology/cg-cat/metadata.xml b/sci-biology/cg-cat/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/cg-cat/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@×××××××××××××××.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@g.o</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>