gentoo resync : 30.05.2020

12 files changed, 84 insertions, 64 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index c80adb185621..36bf0a910f20 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index d122559fffcb..fa184df47818 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1,5 +1,7 @@
+AUX abyss-2.0.3-prog-AR.patch 350 BLAKE2B 20e1a428ea02c3c67c5df9b92f623ddea58f2054912d0ca788f0a9890057277cd98babe48d089852541db262ab0a69e95ead2a4b31456a62597ae1d4856e8c5e SHA512 747e9d258767c698a95615ae83db18662ec1851c0a6dfcdcec6aea68dc76415e89b3f85f1f8ff6c04fff22052c787a43948f8f3588220e2dc66cc7262788c52a
 DIST abyss-2.0.2.tar.gz 1036135 BLAKE2B 6781a63203b5e6a1de70837a6dad7c79643d049b4c1e4b827471f2414cc821f82d98f9856518e3c24486e068c584520d0a1852d4e03d26247b896c776baaee41 SHA512 b19325b9d51e80378fc9818942c4005c94f470f0ad8ff6c1b8b593ad0216d35f9a99c0aa7c627082372690a6a7094ced8ca8efeb0bff6014ca46a67d7eb16a30
 DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570
 EBUILD abyss-2.0.2-r1.ebuild 1255 BLAKE2B 80695f29e6568b78c8243277ac1baecfccc9c6d1f2100fe45c7f6ecc3aa1308b16e5b661c74eb3f5c2b6273c161953cfd2257f0eb1c9e232a5d2eca8dfcb297f SHA512 2a75296cc2d5884be09ce2aa6280af3e54735501125da0dea4cbd297f18061a94ac1ced98990087c209f196c8f624b4cae24c7f7c383913b59ba0c51e9823ed9
+EBUILD abyss-2.0.3-r1.ebuild 1555 BLAKE2B 113efb423e315a0b4abf19b8a75326a90f8da5b88db1d0a5bd5485d6eead927dc7b72398452a0794edf5ec9a2c0dffabf6fe4f15aaa66f48c7cc5e2ca9615c29 SHA512 0ec8921c93ad555f35135f707ae4b71f1e0640e82d81e96a966df755313463c8ddf68991e7602435d5d762ddda8ec5ebc4763bed674985b5cd2cfaefc729a744
 EBUILD abyss-2.0.3.ebuild 1236 BLAKE2B d0150a7fbeddac711b1f3dff0f8b679132d97e6637debb980bd691e0b8fc5d26465cd2dd2c08a8ca389f656006039350b9c4ce8ef53190bce224eb9b0b2e73e5 SHA512 e2b66426eb8b68d32b0afdae3371216cf574270c894d6c71ff0591310d65a1d688dcde6760c31a5372fb7f56cb33331d5a63b23e95cad177172bb26a639884a5
 MISC metadata.xml 572 BLAKE2B 987284bc0e435174f2592854cf67e44d155b64975a65d69fc988352f9bf0c06bfa412bcbba0e3a5a4819a846d5fd1c5695627b8b75ab7c955abff1b0bb4ad76e SHA512 b7461a55a1f34d22b8faceb40c15f66d7564a5fd3ccd626533972f25fcca36f8ce47e7edc5e96e7eab6c9bfc27ac4e094b419c241b7cc4de051025e1a9522198
diff --git a/sci-biology/abyss/abyss-2.0.3-r1.ebuild b/sci-biology/abyss/abyss-2.0.3-r1.ebuild
new file mode 100644
index 000000000000..800a45964cd0
--- /dev/null
+++ b/sci-biology/abyss/abyss-2.0.3-r1.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+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/"
+SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp misc-haskell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-cpp/sparsehash
+	dev-libs/boost:=
+	misc-haskell? (
+		dev-libs/gmp:0=
+		virtual/libffi:0=
+	)
+	mpi? ( sys-cluster/openmpi )"
+DEPEND="${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
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+src_prepare() {
+	default
+	sed -i -e "s/-Werror//" configure.ac || die #365195
+	sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+	eautoreconf
+}
+
+src_configure() {
+	# disable building haskell tool Misc/samtobreak
+	# unless request by user: bug #534412
+	use misc-haskell || export ac_cv_prog_ac_ct_GHC=
+
+	econf $(use_enable openmp)
+}
diff --git a/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch b/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch
new file mode 100644
index 000000000000..d41c58ad261a
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-2.0.3-prog-AR.patch
@@ -0,0 +1,11 @@
+https://bugs.gentoo.org/725300
+--- a/configure.ac
++++ b/configure.ac
+@@ -17,6 +17,7 @@ AC_CHECK_TOOL(GHC, ghc)
+ AM_CONDITIONAL([HAVE_GHC], ["$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/bioruby/Manifest b/sci-biology/bioruby/Manifest
deleted file mode 100644
index 074f6e0d532d..000000000000
--- a/sci-biology/bioruby/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST bio-1.5.1.gem 1445376 BLAKE2B 4de704293ed1c4dee7edc9c86df4ddd35f66eb4433a339fadb58c3f877206e240a8b1dfe6aa8ccd92f0edf9d0f28825cc2b58e33f817fec6bab39e3162f179cf SHA512 822ac6c3d85847193fc1992087abc868e4d1a7cfca82da6ab1830af2927a2a582c3993bc681e129a6aac224ed1cb0b33056d8cc02d3e36d68c9d6a4153c321ca
-DIST bio-1.5.2.gem 1447424 BLAKE2B 6377f7c546faef188d43b1e612f1924f5ab2db3a0017fac1f1b124b6cdf7caf4b66dde53d957d0a733601e3c928f0a84b18ae9da930f4a4908ab236f9365d385 SHA512 a0c4be950ef2983f07e8b9d0ac217310d80d91139ca0edb0263d8ae0a35e62fc07a21861ab26d8bace40003f0d9de4dce1be8f02c7d6d0f4afe3eb3debe3d5cd
-EBUILD bioruby-1.5.1.ebuild 431 BLAKE2B 1f9a60a70312debc75c6eb47bc66e8eaa350fdd8898991bb2c8c0ef59ceb4364c6be308e4bb09f5ba1f641bab824795fdb22a77c22f38754d6e18b9094e3a081 SHA512 b039590a84df3d382f1d0eab42c9a0c6fc7752403a6b158b316746d872cc924a698f80350ddf3decca3641f9c549921d40d23e72798d2d73f4a3fcfbcebe005e
-EBUILD bioruby-1.5.2.ebuild 428 BLAKE2B 30a8bf534852ae88ea37edc4494a1b10c1d6a454306b437c6dde169c322f9175cadff5397934d6a13bd67848591d424beaa9ac2d563a8d5ff95005dcb7569932 SHA512 f01f0361e95660090d0127289e8c3a61c5581cc60cc1c1c82fe25a7b934760ddb965eeb81aca44b265995e135ee6d2f9be755d1bb52aa9ae29df78b400d0aa6a
-MISC metadata.xml 261 BLAKE2B 3768c926bca545090342a947ba83e706a8954c51b99a5e7b3476ba5198cd326fe1c3b8efb51dfd6be1800682556b8ceea065e388981463ab32f3d687951872f3 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a
diff --git a/sci-biology/bioruby/bioruby-1.5.1.ebuild b/sci-biology/bioruby/bioruby-1.5.1.ebuild
deleted file mode 100644
index 036b3be29b37..000000000000
--- a/sci-biology/bioruby/bioruby-1.5.1.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby23 ruby24"
-
-RUBY_FAKEGEM_NAME="bio"
-
-RUBY_FAKEGEM_EXTRAINSTALL="etc"
-
-inherit ruby-fakegem
-
-DESCRIPTION="An integrated environment for bioinformatics using the Ruby language"
-LICENSE="Ruby"
-HOMEPAGE="http://bioruby.org/"
-
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 ~ppc x86"
-
-ruby_add_rdepend "dev-ruby/libxml"
diff --git a/sci-biology/bioruby/bioruby-1.5.2.ebuild b/sci-biology/bioruby/bioruby-1.5.2.ebuild
deleted file mode 100644
index 7977f4073da5..000000000000
--- a/sci-biology/bioruby/bioruby-1.5.2.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby23 ruby24"
-
-RUBY_FAKEGEM_NAME="bio"
-
-RUBY_FAKEGEM_EXTRAINSTALL="etc"
-
-inherit ruby-fakegem
-
-DESCRIPTION="An integrated environment for bioinformatics using the Ruby language"
-LICENSE="Ruby"
-HOMEPAGE="http://bioruby.org/"
-
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 ~ppc x86"
-
-ruby_add_rdepend "dev-ruby/libxml"
diff --git a/sci-biology/bioruby/metadata.xml b/sci-biology/bioruby/metadata.xml
deleted file mode 100644
index 8417d1580d40..000000000000
--- a/sci-biology/bioruby/metadata.xml
+++ /dev/null
@@ -1,8 +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>
-</pkgmetadata>
diff --git a/sci-biology/clustalx/Manifest b/sci-biology/clustalx/Manifest
index 110d0f5eeb0c..506adc0651d3 100644
--- a/sci-biology/clustalx/Manifest
+++ b/sci-biology/clustalx/Manifest
@@ -1,5 +1,5 @@
 AUX clustalx-2.1-qt5.patch 8173 BLAKE2B dca2d4f7531ac38510cc9c2aa788244293c436940d38945c906c76b7a29d395179190833517c01cbe48d450111d3f115427fb55536ab55dd01fc0617ff9e7bc2 SHA512 d8c9e9e1aade86f6ba4aa88618ace305152b819cf445119c82b4d4e56c7923e25876c83fd74c8dc91715ce484ff0ea3111b13ed7d8219c1222ad60e09b72d29e
 DIST clustalx-2.1.tar.gz 341649 BLAKE2B 43a740b278127d4745699a75479e422cc95a864bd55a9fe37eb68c0b36ae89e07848e8fdae2207ff9b3850eebc273b803df0261eefd3e7d96d8fa58c75af3adc SHA512 e8cbad783722161de6999ab01a91d555fc10db609197a8d2878f91e9d7dc998784c02d2ccb54c4936ee27b41321db6f4f37021221662f483b8b6d945b6e1c026
 DIST clustalx.png.xz 74808 BLAKE2B 3e0b7ba5d0c4e1013a1ea0146460384279e7116cccde1abdd2e34de16867d83b88c0a04fbc64524e340611fdc5a5df4dbc73f10af610a43fae65c0907b7ac25d SHA512 0907710c944fc1b883c58501cd7bc2abbc5bf171495b58dbe9829d60d7c3530c210f89a5bfafc3cec03808ae50f5c9a78ce37b9175c2e37590494e115e8e343a
-EBUILD clustalx-2.1-r3.ebuild 1334 BLAKE2B 0b1569dc3212ce64a0441829f9055db197986478a84f690b5211ea2fa3638b066fa2b6e34374fa335c49649bd0c01e1a6df5c5322fda0e734ad26c06b91855fe SHA512 b89c27b5c4169f00029102eefc46c6d0bccf81d25d95201ed87bdf0bf8c9b292bc678e08c129bd24e6bb0b304a49549be861c5a322b8e78626c994472dfcf84e
+EBUILD clustalx-2.1-r3.ebuild 1335 BLAKE2B 699de7fc342e8446cc26d4df33f4160f12a8db5296a3c7da5dbfd925d574888e9b29d6ebafa2ffe01b3f226d76294dc0757409b342bccfe03d85dbbb3e47409d SHA512 089251d547375351d37d244d52dd98b649f6e19cf985fa4f631c68aa8e59f760537d6209c84eac1a5bb2d6381931c21993dce8fd4a812efcbe80a04b3e8b4163
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/clustalx/clustalx-2.1-r3.ebuild b/sci-biology/clustalx/clustalx-2.1-r3.ebuild
index 4a3199f352c9..bd9b57aabe79 100644
--- a/sci-biology/clustalx/clustalx-2.1-r3.ebuild
+++ b/sci-biology/clustalx/clustalx-2.1-r3.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit desktop qmake-utils
 
 DESCRIPTION="Graphical interface for the ClustalW multiple alignment program"
-HOMEPAGE="http://www.ebi.ac.uk/tools/clustalw2/"
+HOMEPAGE="https://www.ebi.ac.uk/Tools/msa/clustalw2/"
 SRC_URI="
 	http://www.clustal.org/download/current/${P}.tar.gz
 	https://dev.gentoo.org/~jlec/distfiles/${PN}.png.xz"
@@ -40,7 +40,7 @@ src_prepare() {
 		-e "s|clustalx.hlp|${EPREFIX}/usr/share/${PN}/clustalx.hlp|" \
 		-i HelpDisplayWidget.cpp || \
 		die "Failed to patch help file location."
-	rm -rf usr || die
+	rm -r usr || die
 }
 
 src_configure() {
diff --git a/sci-biology/foldingathome/Manifest b/sci-biology/foldingathome/Manifest
index a3762634a224..5d7c44f7ad49 100644
--- a/sci-biology/foldingathome/Manifest
+++ b/sci-biology/foldingathome/Manifest
@@ -1,6 +1,6 @@
 AUX 7.3/folding-conf.d 339 BLAKE2B 93a0b3672777ad737ce27694aaca547634c375e180ad3c28c3adb9cae2cb1c054ff9458ee1fe04b70fe9841ae67d41198bcecfc4826d05d5de8df2759bd80910 SHA512 6fd10dc938262c05831e68176e93a24869bb6991508bcc48ece487b701788026561d073025bd347cd77ede13ca26f6b284861f30b07becf72ea77e4db22867b3
 DIST fahclient_7.5.1-64bit-release.tar.bz2 3438239 BLAKE2B 69fb60cdd5356fe4f5ad1f106b67d078baf0394c5d3c474dff2f1ac840bcb31bfd9ca9a9c6112b9ee9497dcdc223732627a21c50b455e46c096a52587d5d229b SHA512 5f6f2f882d57fe53ad0a55b48f09fc3803af6aebbbf0e92be39477d4c4da92237d6edabec61dd8183678bdcfe3923ff9b0938647a77edc2c69ce8958defcfdf1
-DIST fahclient_7.6.9-64bit-release.tar.bz2 3962851 BLAKE2B 896ca7cdd1357bb37cd8a5c438223c398c5f8c6bde7f7302d0e62ccff603b9a3dd3fb348bd021b9654867eb8f2579c91cfe87e3229b365620b383a4f261ae5f4 SHA512 0a360d8a985d3d538922a2d9519b70845a568f7d052c3047e7f847865165e9cd6e741016ee00496161ca3c2115beef34e95ab594d0f864bccc0fe12de6886f19
+DIST fahclient_7.6.13-64bit-release.tar.bz2 3951134 BLAKE2B 2748b7c1987d166bdda08caf5ff2f331523ff519e24768cd7e111c6d3a93f54c10c88d8adbf733230b6c51547360135dbcb272e5d43fd06d01918481601382a1 SHA512 f39f2990d78d075e1061ceaff9453b703a000770a3422965b7b8a91d1814f8804837628d8a34be5afd914228ef787f699f2488523baad295a8d9c1e3bb4f35cf
 EBUILD foldingathome-7.5.1-r3.ebuild 4454 BLAKE2B 9103461fe2614c5494648827b461cc488e7345f3ad12d45ccda6c44c81de7f700120d582b3ab4371974a5a25a62626b535849e8bafa13ac577c59364102cb7a3 SHA512 4c1a451a5df2e2015594f266761d51b9ac0978711ce93f4bc922937a0fa474bdead787926541ad42d554130cf6168e367f8c090648d52951ca6b7f1533c042f2
-EBUILD foldingathome-7.6.9.ebuild 4422 BLAKE2B 50f39d12b3c1bf23e94119a7d3a1434f7f44e1765ab77550e4561875be2e1b5b8ca1e00393ba1b218ebb12f54b4cc27721ee46586986b8771b8216ab6fe20e33 SHA512 1be3543d064a478e22abf386bdc634f5e63710aaada32fd035b4f5c1ef02bc01521a084430e9cc4fed17a677b51a62d811f5c74b1dca1b581b489f585d5d58ee
+EBUILD foldingathome-7.6.13.ebuild 4422 BLAKE2B 50f39d12b3c1bf23e94119a7d3a1434f7f44e1765ab77550e4561875be2e1b5b8ca1e00393ba1b218ebb12f54b4cc27721ee46586986b8771b8216ab6fe20e33 SHA512 1be3543d064a478e22abf386bdc634f5e63710aaada32fd035b4f5c1ef02bc01521a084430e9cc4fed17a677b51a62d811f5c74b1dca1b581b489f585d5d58ee
 MISC metadata.xml 360 BLAKE2B c0ef2b11cc9e6498a420dcd2e6c83ee71f7e286c3e78218257c56350bd2c0921732d48cc4207a31bcfd965a4a9dca65e9bdc4d62831dc430e86541d36fc691f8 SHA512 687f1516a8ec80270fa173b0a7d7c259f3f02ffefa69d3175b72e170bd11aeb786563edb43214390a83b6b61b1231e2734124e50bb2a523d1a564bc3b143f00b
diff --git a/sci-biology/foldingathome/foldingathome-7.6.9.ebuild b/sci-biology/foldingathome/foldingathome-7.6.13.ebuild
index ca477a6d6b77..ca477a6d6b77 100644
--- a/sci-biology/foldingathome/foldingathome-7.6.9.ebuild
+++ b/sci-biology/foldingathome/foldingathome-7.6.13.ebuild