gentoo resync : 18.03.2018

5 files changed, 58 insertions, 2 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index c69ead06b946..4eb3282ae5ff 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index 5446f5063e79..d122559fffcb 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1,3 +1,5 @@
 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.ebuild 1236 BLAKE2B d0150a7fbeddac711b1f3dff0f8b679132d97e6637debb980bd691e0b8fc5d26465cd2dd2c08a8ca389f656006039350b9c4ce8ef53190bce224eb9b0b2e73e5 SHA512 e2b66426eb8b68d32b0afdae3371216cf574270c894d6c71ff0591310d65a1d688dcde6760c31a5372fb7f56cb33331d5a63b23e95cad177172bb26a639884a5
 MISC metadata.xml 572 BLAKE2B 987284bc0e435174f2592854cf67e44d155b64975a65d69fc988352f9bf0c06bfa412bcbba0e3a5a4819a846d5fd1c5695627b8b75ab7c955abff1b0bb4ad76e SHA512 b7461a55a1f34d22b8faceb40c15f66d7564a5fd3ccd626533972f25fcca36f8ce47e7edc5e96e7eab6c9bfc27ac4e094b419c241b7cc4de051025e1a9522198
diff --git a/sci-biology/abyss/abyss-2.0.3.ebuild b/sci-biology/abyss/abyss-2.0.3.ebuild
new file mode 100644
index 000000000000..ccce937c77ce
--- /dev/null
+++ b/sci-biology/abyss/abyss-2.0.3.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2018 Gentoo Foundation
+# 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
+	)"
+
+# 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/clustalx/Manifest b/sci-biology/clustalx/Manifest
index aae876b740a0..f761ea81363f 100644
--- a/sci-biology/clustalx/Manifest
+++ b/sci-biology/clustalx/Manifest
@@ -3,5 +3,5 @@ DIST clustalx-2.1.tar.gz 341649 BLAKE2B 43a740b278127d4745699a75479e422cc95a864b
 DIST clustalx.png.xz 74808 BLAKE2B 3e0b7ba5d0c4e1013a1ea0146460384279e7116cccde1abdd2e34de16867d83b88c0a04fbc64524e340611fdc5a5df4dbc73f10af610a43fae65c0907b7ac25d SHA512 0907710c944fc1b883c58501cd7bc2abbc5bf171495b58dbe9829d60d7c3530c210f89a5bfafc3cec03808ae50f5c9a78ce37b9175c2e37590494e115e8e343a
 EBUILD clustalx-2.1-r1.ebuild 1093 BLAKE2B 369910c48ad315148d210bf616980a483ca37ec9a27e227876e4057faed667db1ca4bc8dfd760dcce2ccb1d54a3fa7d4fdf3d762bdc7b89908c8bdcbcd2610e6 SHA512 997c71482dff6f73841ba912904b9ea34992ffd9dc90466e233017857a93c11a2f930ff242bfc0b1309bedbf4e6be2556bf26efa9a9f7dfe83d0e96abc06e8a0
 EBUILD clustalx-2.1-r2.ebuild 1225 BLAKE2B 458fb581439821d8eabffc507148a830a74e593f84679757699348d65f1bbe076e5fcba21f0fd2d083256d0de63498378ab87f4a3d74d5f3166fbddd93437954 SHA512 6d0d46521bc2511dca32363e7faf6ff550de74f6e6fcf22f0d3ebd7cbe0f10884dbdb52fcfcba034b4185419d2109663bf1e589d072937b6bbc012fe5ad5c250
-EBUILD clustalx-2.1-r3.ebuild 1336 BLAKE2B 0116719c2b776feedeaae20148ee41c5b8cc1d3ddcb006f1899f0db198d2c8e8ab4b8dc8813a806775c367db2a863df769032f02e35584c3aadef78c60f1f90f SHA512 587d03c86f6faf24bbb49cbc9328923fd9d9634a1bd2360669d1c2e25329ad996c6bc63c717af044fc816f009bab482953a5efcb0d11adff161664da930b1fc6
+EBUILD clustalx-2.1-r3.ebuild 1335 BLAKE2B 03ef2401f491e0bec656d6454282009295fb15cfba8e87b8ea113a7276497223272ac6be2d4382030ba777355cdc905dad8a7fc375bb08b58b42bc6f912151be SHA512 28fa3b11103b78dba8d15dd1b43e18dcfce575c141f880dcf74230f396fe80a4bf684b4abad3ab74eaceb578625ea0727d7afc50d86f789a1c6f682a9cb46b39
 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 0f9366bee7f5..5fe34efb5f8a 100644
--- a/sci-biology/clustalx/clustalx-2.1-r3.ebuild
+++ b/sci-biology/clustalx/clustalx-2.1-r3.ebuild
@@ -13,7 +13,7 @@ SRC_URI="
 
 LICENSE="GPL-3 LGPL-3"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="amd64 ~x86"
 IUSE=""
 
 DEPEND="