From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Mon, 9 Oct 2017 18:53:29 +0100
Subject: reinit the tree, so we can have metadata

---
 sci-biology/abyss/Manifest              |  5 +++
 sci-biology/abyss/abyss-2.0.2-r1.ebuild | 55 +++++++++++++++++++++++++++++++++
 sci-biology/abyss/metadata.xml          | 18 +++++++++++
 3 files changed, 78 insertions(+)
 create mode 100644 sci-biology/abyss/Manifest
 create mode 100644 sci-biology/abyss/abyss-2.0.2-r1.ebuild
 create mode 100644 sci-biology/abyss/metadata.xml

(limited to 'sci-biology/abyss')

diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
new file mode 100644
index 000000000000..53cbd51fdb65
--- /dev/null
+++ b/sci-biology/abyss/Manifest
@@ -0,0 +1,5 @@
+DIST abyss-2.0.2.tar.gz 1036135 SHA256 6482b81eb5439703c0dbf6cd7ac25cd0df7541d9e04ef7865343b241e21db460 SHA512 b19325b9d51e80378fc9818942c4005c94f470f0ad8ff6c1b8b593ad0216d35f9a99c0aa7c627082372690a6a7094ced8ca8efeb0bff6014ca46a67d7eb16a30 WHIRLPOOL 23447cb00b0bb9b5b8a724ba44f8d7193d9640ccd19956b42bbbd83b67557b66b7c68141d6f292c4ab11ab523286471d5ee1c938f22749a61162de056a0d903e
+EBUILD abyss-2.0.2-r1.ebuild 1255 SHA256 76cd126c146ca100d00fe6b48b8a9a2bfcdef7db9dabfcb7ab6eccbeaa3d7c68 SHA512 2a75296cc2d5884be09ce2aa6280af3e54735501125da0dea4cbd297f18061a94ac1ced98990087c209f196c8f624b4cae24c7f7c383913b59ba0c51e9823ed9 WHIRLPOOL d50d12d60d22f98d320a42693de9eef945d64067ac0b5cf25cfc24b8b657789b04b8e08c9ab133a3683b0486b8d0441ec35d2c7d24eb1f2930e78ca152d84d2f
+MISC ChangeLog 5076 SHA256 033515486551f430c662c0f8f24932c83fbd40ce3dc20fc487aad8b2449d93e3 SHA512 b16c9e47c2af4c8dcdf421f487aa4d665b3658457fc77a19f41bc62b7d12df756f7fd0d5c0ff2e03b0c3dd4558414126be15c0c6e9cff10d06c4e1e45871bb21 WHIRLPOOL 45db002d9a6e585df0460ab09fd046d6dab8cda26a81aba849793ed1d0c54ce13330b7963274d633410934d6f7d6c405a91f145c33239afb6082fe865449288e
+MISC ChangeLog-2015 3086 SHA256 3e295bd3a13f20016e1baaf773c888fad647ad1aa09f77719590a3d01b33e320 SHA512 28de3b6bb48d775fb1ecd1bcc37aadf43451a7200ce691b11833a41dcdde6046e70e7a3b76d5fecb2cadcd96fd94d3e67b6ad1758b9132028aac19339c8e9bd4 WHIRLPOOL 9d73031727499d87e932b55833512068e36c57ca6ab4dc06d8a458f3db89fefda263d858d322468f6de5a9a34113f1a826a01878c633d19ed3d79d962ba410ff
+MISC metadata.xml 572 SHA256 5649b00a9f038a5916a2205b92cf55df64d886a7451362d2ad481d09dd53f412 SHA512 b7461a55a1f34d22b8faceb40c15f66d7564a5fd3ccd626533972f25fcca36f8ce47e7edc5e96e7eab6c9bfc27ac4e094b419c241b7cc4de051025e1a9522198 WHIRLPOOL cd121dd5eeb4084400bc72b6c9af38076b064d5f12b19fe7964a592fdd881fd1bafd4cd8a2389d9ba5a03a99762452e2f53d7898916b09e258692d24a23a24c9
diff --git a/sci-biology/abyss/abyss-2.0.2-r1.ebuild b/sci-biology/abyss/abyss-2.0.2-r1.ebuild
new file mode 100644
index 000000000000..0d1c14ac265e
--- /dev/null
+++ b/sci-biology/abyss/abyss-2.0.2-r1.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2016 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
+		dev-haskell/mmap
+	)"
+
+# 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/metadata.xml b/sci-biology/abyss/metadata.xml
new file mode 100644
index 000000000000..47116e507d89
--- /dev/null
+++ b/sci-biology/abyss/metadata.xml
@@ -0,0 +1,18 @@
+<?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>
+  <maintainer type="project">
+    <email>haskell@gentoo.org</email>
+    <name>Gentoo Haskell</name>
+  </maintainer>
+  <use>
+    <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag>
+  </use>
+  <upstream>
+    <remote-id type="github">bcgsc/abyss</remote-id>
+  </upstream>
+</pkgmetadata>
-- 
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