gentoo resync : 16.01.2021

12 files changed, 14 insertions, 323 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 7adf00a4e082..cb256061da9a 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index 72c889e36a57..fe1e04ce4b56 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1,4 +1,3 @@
-AUX abyss-2.0.3-prog-AR.patch 350 BLAKE2B 20e1a428ea02c3c67c5df9b92f623ddea58f2054912d0ca788f0a9890057277cd98babe48d089852541db262ab0a69e95ead2a4b31456a62597ae1d4856e8c5e SHA512 747e9d258767c698a95615ae83db18662ec1851c0a6dfcdcec6aea68dc76415e89b3f85f1f8ff6c04fff22052c787a43948f8f3588220e2dc66cc7262788c52a
-DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570
-EBUILD abyss-2.0.3-r2.ebuild 1556 BLAKE2B a25f93323564ce83b2a15ed31881a873ddafe688f9277439aef25dbb3a76c6d796984105498c2f547bf00229ce4c465d9e5c22c949c543b29fd61c22a8d52568 SHA512 9c5649115d97c8b6aee3909d092f8429c59c31b9200b71023bb05e3bc2501c3f55a1d4b07c9bacbfd94fc6a10a4a5124a6135b743e29d126856796bab5ea1f3f
+DIST abyss-2.3.4.tar.gz 3511137 BLAKE2B 2b7449233055d22330f44951f9f6d5ff1a116fa3e19c09c17cd4fa517d2fc055c4f00ccb82c7e09b1b939ac6f7a1caf73cf73c33bd3c8aa9ff11879c227a2aaa SHA512 9d4e418399dd62883b53e831f51a0bd2ba228da73eda6c6459cd729c002eb0487f9613fca1c9bd0f4fbb076eed8a9b952505ee97143ab7dde537c23e4a246cd4
+EBUILD abyss-2.3.4.ebuild 1269 BLAKE2B bf4a1edb477650f3d6650c7ae1cfb0d37132215bf8bb4c395a702c506a0d648386168731ad329875380fd46f1a3ccbe673d3211d1ee854538bbe28dbeb49ecb5 SHA512 26a5fec0fbed0c0fdb0f328b993553ec1ceb7632d2d9ad18736f3099df542a88da0d1996c444d3fdbfe59d1dda55161e7de8ea121a22a1bb80c507656999d39c
 MISC metadata.xml 457 BLAKE2B 7941e6d318c33992a00ce167bf738bea01a1c54b3e8381947757880e34f5a38da9bbd91837a34338f81e6d23e363dbbde734cb5075f6bfcf49a694f19d5a24a8 SHA512 e722cef310475d7e4aae8b0a9e23c73c0ab44acf62e6afdb4355da201565aedbedd2f2100676c6c58218909d60b45b1938c3afe13fff62c4fdfbea0ff2ef6e49
diff --git a/sci-biology/abyss/abyss-2.0.3-r2.ebuild b/sci-biology/abyss/abyss-2.3.4.ebuild
index b9aed09d3eec..c2e1ffd29b32 100644
--- a/sci-biology/abyss/abyss-2.0.3-r2.ebuild
+++ b/sci-biology/abyss/abyss-2.3.4.ebuild
@@ -1,17 +1,17 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 inherit autotools toolchain-funcs
 
 DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
+HOMEPAGE="https://www.bcgsc.ca/resources/software/abyss/"
 SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
 
-LICENSE="abyss"
+LICENSE="GPL-3"
 SLOT="0"
-IUSE="+mpi openmp misc-haskell"
+IUSE="openmp misc-haskell"
 KEYWORDS="~amd64 ~x86"
 
 RDEPEND="
@@ -21,24 +21,17 @@ RDEPEND="
 		dev-libs/gmp:0=
 		dev-libs/libffi:0=
 	)
-	mpi? ( sys-cluster/openmpi )"
+	sys-cluster/openmpi
+	dev-db/sqlite:3
+"
 DEPEND="${RDEPEND}
 	misc-haskell? (
 		dev-lang/ghc
-	)"
-
-PATCHES=("${FILESDIR}"/${PN}-2.0.3-prog-AR.patch)
-
-# GHC uses it's own native code generator. Portage's
-# QA check generates false positive because it assumes
-# presence of GCC-specific sections.
-#
-# Workaround false positiove by disabling the check completely.
-# bug #677600
-QA_FLAGS_IGNORED='/usr/bin/abyss-samtobreak'
+	)
+"
 
 # todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
+# todo: also allow build with mpich (--enable-mpich)
 
 pkg_pretend() {
 	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
@@ -60,5 +53,5 @@ src_configure() {
 	# unless request by user: bug #534412
 	use misc-haskell || export ac_cv_prog_ac_ct_GHC=
 
-	econf $(use_enable openmp)
+	econf $(use_enable openmp) --enable-maxk=256
 }
diff --git a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch b/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch
deleted file mode 100644
index d41c58ad261a..000000000000
--- a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-https://bugs.gentoo.org/725300
---- a/configure.ac
-+++ b/configure.ac
-@@ -17,6 +17,7 @@ AC_CHECK_TOOL(GHC, ghc)
- AM_CONDITIONAL([HAVE_GHC], ["$GHC" --version])
- AC_CHECK_PROG(PANDOC, pandoc, yes)
- AM_CONDITIONAL([HAVE_PANDOC], [test x"$PANDOC" = x"yes"])
-+AM_PROG_AR
- 
- # Checks for header files.
- AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \
diff --git a/sci-biology/gibbs/Manifest b/sci-biology/gibbs/Manifest
deleted file mode 100644
index 2475c8e59888..000000000000
--- a/sci-biology/gibbs/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX gibbs-3.1-fix-CFLAGS.patch 213 BLAKE2B 9a0f7f0412569cef1cce984f5087f7b99e16163ac6c6c3e0aad27f14cd2f7ed5bfb22f21f433f1c343a9e73899dedb00ea93467adc4cc42a3dceae41aa1e3f86 SHA512 afd0fffb891eefe8799025a032a802f398ac737900e1fac86f79964bfe493ee906c3e5f42abc5e45d3de5af80887ab25ef207a885a6ddb8b6fe0d0ab1f906046
-DIST gibbs-3.1.tar.gz 563300 BLAKE2B 74b97407ccdac49d19dd2fa5fe3a5384b52a3ae871f197c1212e818fb7ce2307f2d04a91cf8a1d14c82d57b6f7266bbae849091bec9e580b8d473b595a836212 SHA512 b1ffc0d0c7debaced3c3d850eb7d2c42e13358d1e7c6ff5e6be0273446edc50bd655c52c5ae904a9054d47d7a48abd54a7684534ba7681375b657ad77fb8cb52
-EBUILD gibbs-3.1.ebuild 912 BLAKE2B 29d51a769e6a477bb81da6d467a1b2befbfd2f83282184a1087de0a4a5d736a5df01f3767663141bd6282826bd4fcad5ca0ddaea916fc93e582ccd8b4a8e98b8 SHA512 975c0bd3c57a8db25324636ce8f2fd9ef9bde1de4a980ba93fbe3e7bf8362a51f06ae5b1687570d81012ef6eed6536bfde418327a045bcf54a1e1517d85d989f
-MISC metadata.xml 484 BLAKE2B d9cd3734d282126d0c50a2b4ac64e5f7dc584150e47a02fad550b3b4e3102018d95c0d226967dae006523ed37da4f3b33a89e6911d237aed54af8a923c7d5f45 SHA512 9a540d968cae036719647f394219ec70184bf956d1c6e6b86e32218426800bad998619e11094ca0d80714b6bbf5b9f37c3edc1397755e0c34bc8b63a16a43655
diff --git a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch b/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch
deleted file mode 100644
index 6eaad637cfc8..000000000000
--- a/sci-biology/gibbs/files/gibbs-3.1-fix-CFLAGS.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/configure.in
-+++ b/configure.in
-@@ -51,7 +51,7 @@
- 	fi

- 	])

- 

--CFLAGS="$OPTFLAGS $MPIFLAGS  -Wall -Werror $MACFLAG"

-+CFLAGS="$CFLAGS $OPTFLAGS $MPIFLAGS -Wall $MACFLAG"

- 

- AC_PROG_CC([$COMP_LIST])

- 

diff --git a/sci-biology/gibbs/gibbs-3.1.ebuild b/sci-biology/gibbs/gibbs-3.1.ebuild
deleted file mode 100644
index a06d0880ee4d..000000000000
--- a/sci-biology/gibbs/gibbs-3.1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools
-
-DESCRIPTION="Identify motifs, conserved regions, in DNA or protein sequences"
-HOMEPAGE="http://bayesweb.wadsworth.org/gibbs/gibbs.html"
-SRC_URI="mirror://gentoo/gibbs-${PV}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="mpi"
-
-DEPEND="
-	mpi? (
-		virtual/mpi
-		sys-cluster/mpe2
-	)"
-RDEPEND="${DEPEND}"
-
-PATCHES=( "${FILESDIR}"/${PN}-3.1-fix-CFLAGS.patch )
-
-src_prepare() {
-	default
-	mv configure.{in,ac} || die
-	eautoreconf
-}
-
-src_configure() {
-	use mpi && export CC=mpicc
-	econf $(use_enable mpi)
-}
-
-src_install() {
-	default
-
-	exeinto /usr/$(get_libdir)/${PN}
-	doexe *.pl
-}
-
-pkg_postinst() {
-	einfo "Supplementary Perl scripts for Gibbs have been installed into ${EROOT}/usr/$(get_libdir)/${PN}."
-	einfo "These scripts require installation of sci-biology/bioperl."
-}
diff --git a/sci-biology/gibbs/metadata.xml b/sci-biology/gibbs/metadata.xml
deleted file mode 100644
index a0cd7b42b3ab..000000000000
--- a/sci-biology/gibbs/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<longdescription>
-		The Gibbs motif sampler stochastically examines candidate alignments
-		in an effort to find the best alignment as measured by the maximum
-		a posteriori (MAP) log-likelihood ratio.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest
deleted file mode 100644
index 82fc7ef9c66e..000000000000
--- a/sci-biology/picard/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX 1.103-gentoo.patch 5667 BLAKE2B 7d096dfb289a121a9e4cd27614dbf106fcbd17ea39666dd11508c7e58ec098c653c6bfb60ce69f173e3da25963c5d7335affb659566cf43d26f287d2898c37b2 SHA512 966b0cc9ffc5bbf4b23c003538e01533344df496c38797ab84fcd2b382e91e003cc797a0c6ff5a878406b1fc169c1b044bce447b68770c665cec327762f08f6d
-DIST picard-1.103.tar.bz2 15037887 BLAKE2B a4df3aad9242749964a997698d80634e14ce19af575de9609655483eba247d0968cbdc856dbf00d854ec7eae37da8f3d047c50e4b78843e9d08441d9ef18eff6 SHA512 f8db38a8fee278868cd2ea11f78275a5defadf36e053703133f0f90836df8e3a3ca08635fd7c02967ed99b52bc5baffa600a34b58a94288d3eede7f5c3dd79ca
-EBUILD picard-1.103.ebuild 1513 BLAKE2B 1755995201677c74108fbc0af289b46c1c518a620b87019adab0f90dd2fa6abc5a4d0135f2883f9716aadb96f60b76199fba109292ae4ff65b29dac82023e119 SHA512 e731bbabeed2d16707ad900a8a271143542c3c851c4becd240d79158b2f806bf5a4faf22b7c466427c406392faefc51628be621ec5b2d429a47a716d003a66c1
-MISC metadata.xml 338 BLAKE2B f32ddb3924bbd34ae207756d7e9b17715cd1b0a87c079201d628cb851c3f1bea487d6953548e1b820148900d0ae2d056ce55408d5d84a4a8f798440b8e4e8a53 SHA512 17119585510e7c19ded9131b140b21c9ae9773e6800d1c2ab56401d15ca995fec7ea3db71d231fc1c90e9f1a22bdc3ed01506fff1411221675c669febde9736b
diff --git a/sci-biology/picard/files/1.103-gentoo.patch b/sci-biology/picard/files/1.103-gentoo.patch
deleted file mode 100644
index 00e89b95056a..000000000000
--- a/sci-biology/picard/files/1.103-gentoo.patch
+++ /dev/null
@@ -1,131 +0,0 @@
-diff --git a/build.xml b/build.xml
-index fca2271..11f4fbd 100755
---- a/build.xml
-+++ b/build.xml
-@@ -52,9 +52,6 @@
-     <property name="testng.verbosity" value="2"/>
-     <property name="test.debug.port" value="5005" />  <!-- override on the command line if desired -->
- 
--    <property environment="env"/>
--    <property name="java6.home" value="${env.JAVA6_HOME}"/>
--
-     <condition  property="isUnix">
-         <os family="unix"/>
-     </condition>
-@@ -78,9 +75,6 @@
-             <pathelement location="${classes}"/>
-         </path>
- 
--        <path id="java6.lib.ref">
--            <fileset dir="${java6.home}/lib" includes="*.jar"/>
--        </path>
-     </target>
- 
-     <!-- CLEAN -->
-@@ -94,10 +88,6 @@
-     </target>
- 
-     <!-- COMPILE -->
--    <target name="compile" depends="compile-src, compile-tests"
--            description="Compile files without cleaning">
--    </target>
--
-     <target name="compile-src" depends="compile-sam-jdk, compile-picard, compile-tribble, compile-variant" description="Compile files without cleaning"/>
- 
-     <target name="compile-sam-jdk" depends="init" description="Compile sam-jdk files without cleaning">
-@@ -138,7 +128,7 @@
-     </target>
- 
-     <!-- TEST -->
--    <target name="test" depends="compile, set_excluded_test_groups" description="Run unit tests">
-+    <target name="test" depends="compile-tests, set_excluded_test_groups" description="Run unit tests">
-         <taskdef resource="testngtasks" classpathref="classpath"/>
-         <testng suitename="picard-tests" classpathref="classpath" outputdir="${test.output}"
-                 failureproperty="tests.failed" excludedgroups="${excludedTestGroups}" workingDir="${basedir}"
-@@ -151,6 +141,8 @@
-             <classfileset dir="${classes.test}">
-                 <include name="**/Test*.class"/>
-                 <include name="**/*Test.class"/>
-+		<exclude name="**/ValidateSamFileTest.class" />
-+		<exclude name="**/VCFWriterUnitTest.class" />
-             </classfileset>
-             <jvmarg value="-Xmx2G"/>
-         </testng>
-@@ -165,7 +157,7 @@
-     </target>
- 
-     <target name="single-test"
--            depends="compile, compile-tests"
-+            depends="compile-tests"
-             description="Compile and run a single test.">
-         <taskdef resource="testngtasks" classpathref="classpath"/>
-         <fail unless="name" message="Please provide input test: -Dname=..." />
-@@ -200,13 +192,12 @@
-         </jar>
-     </target>
- 
--    <target name="picard-jar" depends="compile"
-+    <target name="picard-jar" depends="compile-src"
-             description="Builds picard-${picard-version}.jar for inclusion in other projects">
-         <mkdir dir="${dist}"/>
-         <jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
-             <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>
-             <fileset dir="${src.scripts}" includes="**/*.R"/>
--            <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/>
-             <manifest>
-                 <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/>
-                 <attribute name="Implementation-Vendor" value="Broad Institute"/>
-@@ -214,7 +205,7 @@
-         </jar>
-     </target>
- 
--    <target name="tribble-jar" depends="compile"
-+    <target name="tribble-jar" depends="compile-src"
-             description="Builds tribble-${tribble-version}.jar for inclusion in other projects">
-         <mkdir dir="${dist}"/>
-         <jar destfile="${dist}/tribble-${tribble-version}.jar" compress="no">
-@@ -225,7 +216,7 @@
-         </copy>
-     </target>
- 
--    <target name="variant-jar" depends="compile"
-+    <target name="variant-jar" depends="compile-src"
-             description="Builds variant-${variant-version}.jar for inclusion in other projects">
-         <mkdir dir="${dist}"/>
-         <jar destfile="${dist}/variant-${variant-version}.jar" compress="no">
-@@ -262,7 +253,7 @@
-         </javadoc>
-     </target>
- 
--    <target name="package-commands" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar">
-+    <target name="package-commands" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar">
-         <delete dir="${command_tmp}"/>
- 
-         <mkdir dir="${command_tmp}"/>
-@@ -344,7 +335,7 @@
-     </target>
- 
-     <!-- ALL -->
--    <target name="all" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target">
-+    <target name="all" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target">
-         <zip zipfile="${dist}/picard-tools-${picard-version}.zip">
-             <zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/>
-             <zipfileset dir="${lib}" includes="snappy*.jar"/>
-@@ -468,8 +459,6 @@
-                    target="${javac.target}">
-                 <classpath refid="@{compile.classpath}"/>
-                 <compilerarg line="@{compiler.args}" />
--                <!-- ensure that Java 6 bootclasspath is used -->
--                <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/>
-             </javac>
-         </sequential>
-     </macrodef>
-@@ -494,8 +483,6 @@
-                     <pathelement location="${classes}"/>
-                 </classpath>
-                 <compilerarg line="@{compiler.args}"/>
--                <!-- ensure that Java 6 bootclasspath is used -->
--                <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/>
-             </javac>
-         </sequential>
-     </macrodef>
diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml
deleted file mode 100644
index 22fd62cbaa79..000000000000
--- a/sci-biology/picard/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://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">picard</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/picard/picard-1.103.ebuild b/sci-biology/picard/picard-1.103.ebuild
deleted file mode 100644
index 7a6111c87746..000000000000
--- a/sci-biology/picard/picard-1.103.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="5"
-
-JAVA_PKG_IUSE="doc source test"
-WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java-based command-line utilities that manipulate SAM files"
-HOMEPAGE="http://picard.sourceforge.net/"
-SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="dev-java/snappy:1.0
-	dev-java/cofoja:0
-	dev-java/commons-jexl:2
-	dev-java/ant-core:0"
-
-DEPEND=">=virtual/jdk-1.6
-	dev-java/ant-apache-bcel:0
-	test? (
-		dev-java/testng:0
-		dev-lang/R
-	)
-	${CDEPEND}"
-RDEPEND=">=virtual/jre-1.6
-	${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_TEST_TARGET="test"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core"
-EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng"
-
-java_prepare() {
-	mkdir "${S}"/lib || die
-
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-
-	mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die
-}
-
-src_install() {
-	cd dist || die
-
-	for i in *-${PV}.jar; do
-		java-pkg_newjar $i ${i/-${PV}/}
-		rm $i || die
-	done
-
-	java-pkg_dojar *.jar
-	for i in *.jar; do
-		java-pkg_dolauncher ${i/.jar/} --jar $i;
-	done
-
-	use source && java-pkg_dosrc "${S}"/src/java/*
-	use doc && java-pkg_dojavadoc "${S}"/javadoc
-}
-
-src_test() {
-	java-pkg-2_src_test
-}