Drop masked package - sci-biology/tgicl

Signed-off-by: Justin Lecher <jlec@gentoo.org>

4 files changed, 0 insertions, 67 deletions

diff --git a/profiles/package.mask b/profiles/package.mask
index a148f07be..d57ef61cf 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -32,7 +32,6 @@
 
 # Justin Lecher <jlec@gentoo.org> (24 April 2016)
 # rev dep absent
-sci-biology/tgicl
 sci-mathematics/scilab
 
 # Justin Lecher <jlec@gentoo.org> (24 April 2016)
diff --git a/sci-biology/tgicl/Manifest b/sci-biology/tgicl/Manifest
deleted file mode 100644
index 3bc8a1ce1..000000000
--- a/sci-biology/tgicl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST TGICL-2.1.tar.gz 2925009 SHA256 02682846db9c28a78f5bcfc4ea715dd9e4de8c68b02474d8088831355a3ec989 SHA512 21799b780ab45229ef2afc118ce0ba9f6cd31de5e39093367236f1c7daa20571d287159fd185a42270b546728972ecb831339e4304d25d79fa325fd89ad2c0c8 WHIRLPOOL 3a8ef5db27d053b58c92246c991854741285cfacd6a187d4de0aabb4582b59cd0616fac099f35bde6c074fc40cc5942fc27c4c1b917801f875e3536f27dd32d9
diff --git a/sci-biology/tgicl/metadata.xml b/sci-biology/tgicl/metadata.xml
deleted file mode 100644
index 7fad0fdd2..000000000
--- a/sci-biology/tgicl/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>mmokrejs@fold.natur.cuni.cz</email>
-    <name>Martin Mokrejs</name>
-  </maintainer>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">tgicl</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/tgicl/tgicl-2.1.ebuild b/sci-biology/tgicl/tgicl-2.1.ebuild
deleted file mode 100644
index fdd322d1f..000000000
--- a/sci-biology/tgicl/tgicl-2.1.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit perl-module
-
-DESCRIPTION="TIGR perl scripts for clustering"
-HOMEPAGE="http://sourceforge.net/projects/tgicl"
-SRC_URI="http://sourceforge.net/projects/tgicl/files/tgicl%20v2.1/TGICL-2.1.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
-	dev-perl/Module-Build
-	sci-biology/cap3-bin
-	sci-biology/ncbi-tools
-	sci-biology/cdbfasta
-	sci-biology/clview
-	sci-biology/nrcl
-	sci-biology/psx
-	sci-biology/sclust
-	sci-biology/seqclean
-	sci-biology/tclust
-	sci-biology/zmsort"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/TGICL-2.1
-
-# ignore these binaries: mdust, psx, sclust, tclust, zmsort
-# cdbyank and cdbfasta I think were updated by the author more than once. I am not sure if he has updated the tgi-tools package as well. I can compare the cdbfasta tool with the ones in tgi-tools and see if I find any diffs.
-
-# Also cap3 was a problem because for a long time there was no package for it and it is not an OS product. We got author agreement that we can redistribute his binaries along with tgicl code. From what I see you have a package. It would be great if I can make tgicl depend on a cap3 package at some point. I have to check debian/rh though.
-
-# On a same note, there is a ncbi package and tgicl should depend on that. There is however a problem with mgblast. Old time ago, in a galaxy far, far away, some dark sith lord made a patch for it, patch that never made it back to ncbi developers. Meanwhile ncbi tools kept evolving and the patch is now obsolete and it may break the code. However I hope to entirely drop mgblast for the next tgicl release. I also hope to slowly phase out tclust, sclust, cdbfasta, cdbyank, zmsort, psx, tgicl_asm.psx and tgicl_cluster.psx.
-
-src_install(){
-	./Build install || die "Failed to execute ./Build install"
-	einfo "We have to use the mgblast binary provided by upstream because it cannot be compiled against newer ncbi-tools anymore"
-	einfo "We also keep pvmsx binary because the pvmsx package needs pvm3.h header which is probably the one from pvm bundle which is not in portage at all, contact sys-cluster herd"
-	for f in mdust psx sclust tclust nrcl zmsort cap3 formatdb cdbfasta cdbyank; do rm -f "${D}"/usr/bin/$f || die "Cannot delete ${D}"/usr/bin/"$f"; done
-
-	# fix first lines of teh script to use /usr/bin/perl instead of /usr/bin/perl-$version
-	for f in tgicl tgicl_asm.psx tgicl_asmpta.psx tgicl_cluster.psx; do
-		sed -i 's@^#!/usr/bin/perl-*@#! /usr/bin/perl@' "${D}"/usr/bin/$f || die "Failed to fix ${D}"/usr/bin/"$f";
-	done
-}