gentoo resync : 07.05.2021

7 files changed, 0 insertions, 102 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index fbbd10ceb2b8..c910d9dc7469 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/diya/Manifest b/sci-biology/diya/Manifest
deleted file mode 100644
index 4ad379641896..000000000000
--- a/sci-biology/diya/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST diya-1.0-rc4.tar.gz 386706 BLAKE2B 9d000892c3da9ec307a8e089056611bc9cd566ac2dea046601506215c1a5c5fb67621324d2d9e1de94ee4e00129325448e3a1a8aa417e5d8c07f564a77e287d6 SHA512 64a00cb7f07200882d0b97f58e6b7f26d08ab0eab43834c3d19ab08f61080f8edb4a63833095e876c72c087324d39b2c4334ed1d3aa0280b7efb6a7ab3e08007
-EBUILD diya-1.0_rc4.ebuild 1217 BLAKE2B 014c091e406c0bf0b9a6544abdada049fd29914e72645cbeea820ee152d1eb5edf4137d35e79fd70e0e1ffdb542af78999a80138ec12b49a687764d25aa3a137 SHA512 b375b2561d04f7c74db215f5dc61d7f3dba395e2bc025b392c2d5201938a8f49481698a1d863d9b3f4a8094e6a2244afed21e088f2893f7dc2d51df88cb2c8ca
-MISC metadata.xml 345 BLAKE2B 3f4217699268536e4a5ca038d3fda29296606f96b3bccdfce05fbde987c98f572603555bab4036274dd6a76745692db7f669a36764a80cd2ee1d851ee5221970 SHA512 e7ea850a7f00eddfaeca18fa71baafd495191919211aa4d5a2439e48e57a09a1e383b27b1f1bccd8b2533bc5028bd1ead4ab763a514ed6dda96ca3ff625d2657
diff --git a/sci-biology/diya/diya-1.0_rc4.ebuild b/sci-biology/diya/diya-1.0_rc4.ebuild
deleted file mode 100644
index ae923b60da8d..000000000000
--- a/sci-biology/diya/diya-1.0_rc4.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="5"
-
-inherit perl-module
-
-DESCRIPTION="Do It Yourself Annotation, tools & libraries for sequence assembly & annotation"
-HOMEPAGE="http://gmod.org/wiki/Diya"
-SRC_URI="mirror://sourceforge/diyg/files/diya/diya-1.0/diya-${PV/_/-}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="-minimal"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="sci-biology/bioperl
-	dev-perl/Data-Utilities
-	dev-perl/XML-Simple"
-RDEPEND="${DEPEND}
-	!minimal? (
-		sci-biology/mummer
-		sci-biology/glimmer
-		sci-biology/trnascan-se
-		sci-biology/infernal )"
-
-# see ftp://ftp.ncbi.nih.gov/blast/ to check if blast and blast+ are different from ncbi-tools and ncbi-tools++
-# * rfamscan.pl v0.1      (http://www.sanger.ac.uk/Users/sgj/code/)
-# * UniRef50                              (http://www.ebi.ac.uk/uniref/)
-# * Protein Clusters (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/CLUSTERS/)
-# The file cddid_all.tbl can be found at ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/.
-
-S="${WORKDIR}/diya-${PV/_/-}"
-
-SRC_TEST=do
-
-src_install() {
-	mydoc="INSTALL README docs/diya.html"
-	perl-module_src_install
-	insinto /usr/share/${PN}
-	doins -r diya.conf docs examples scripts
-}
diff --git a/sci-biology/diya/metadata.xml b/sci-biology/diya/metadata.xml
deleted file mode 100644
index 37bde911b940..000000000000
--- a/sci-biology/diya/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">diyg</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/gatk/Manifest b/sci-biology/gatk/Manifest
deleted file mode 100644
index df7ae7e85fe8..000000000000
--- a/sci-biology/gatk/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST gatk-2.4.tar.gz 9106774 BLAKE2B a9ac1602091a2f0902c2841942f8dd739562ef6ebbd35894fa445e6a28d748f3c645936914acbdafc8fa59330149ee5ef0738657d8e78d5cf4af5bd26e37ab6b SHA512 9050fc2024d0b3c9a6b5617787831c0496276bcd7318a872f6c1128c31fc31c6f59429a1b189e5c2cc740909b42d846b5e041f8626b03af3a80442294db34ace
-EBUILD gatk-2.4.ebuild 845 BLAKE2B 49efa9285196e9028f6b25976c019d93b48013ab2a049faa8173d6c0204033c1247eb12303bd08bff8393c50b9b6aee49997546c49a37e2970b41aa529961b68 SHA512 2eacd0d6c4351071e42b87a35e5930502d85dff08c7a67dd5403690ab99d402fc9755464ce7055c5ed69752c27d0304cbd1fc3747a80e73d115e034ceccde2a9
-MISC metadata.xml 349 BLAKE2B 277c979d19162d54c5a762e24fcc90d6fc043e5ddd315824b1ccc2376354db4169690933e9d9ebedaf8589636066bf5b32a646ca28892615e8626d7a8d3c43ac SHA512 1605fb041826c7197edcd3658343ed3ac50aea7dfa53262700b9f9e1a45ee81df501e55bf1e8417201f0f2709b6b6e29bb6e5036b7c187846b4dec5e89903f54
diff --git a/sci-biology/gatk/gatk-2.4.ebuild b/sci-biology/gatk/gatk-2.4.ebuild
deleted file mode 100644
index bab228e77f5f..000000000000
--- a/sci-biology/gatk/gatk-2.4.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-EANT_BUILD_TARGET="dist"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-
-inherit java-pkg-2 java-ant-2 vcs-snapshot
-
-DESCRIPTION="The Genome Analysis Toolkit"
-HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"
-SRC_URI="https://github.com/broadgsa/gatk/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND=">=virtual/jre-1.6"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-	java-pkg-2_src_prepare
-	sed -i '/property name="ivy.home"/ s|${user.home}|'${WORKDIR}'|' build.xml || die
-}
-
-src_install() {
-	java-pkg_dojar dist/*.jar
-	java-pkg_dolauncher GenomeAnalysisTK --jar GenomeAnalysisTK.jar
-	java-pkg_dolauncher AnalyzeCovariates --jar AnalyzeCovariates.jar
-}
diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml
deleted file mode 100644
index 8c1bb65774cc..000000000000
--- a/sci-biology/gatk/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="github">broadgsa/gatk</remote-id>
-  </upstream>
-</pkgmetadata>