gentoo resync : 16.01.2021

3 files changed, 14 insertions, 33 deletions

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 \