From 03ada3844855dd1c9ff2627e7f9239d0248e7cc6 Mon Sep 17 00:00:00 2001
From: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
Date: Thu, 13 Jan 2022 12:19:37 +0100
Subject: sci-biology/abyss: add version 2.3.4

Closes: https://bugs.gentoo.org/646478
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
---
 sci-biology/abyss/Manifest           |  1 +
 sci-biology/abyss/abyss-2.3.4.ebuild | 57 ++++++++++++++++++++++++++++++++++++
 2 files changed, 58 insertions(+)
 create mode 100644 sci-biology/abyss/abyss-2.3.4.ebuild

diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index e03409dd93f2..32cead3a3a6e 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1 +1,2 @@
 DIST abyss-2.0.3.tar.gz 1049144 BLAKE2B 1a320cac735747225723f0d636af435ffcac9efb3273323150f258c0f4c27ed81bb104cb06a726aa664118cc9d2224b745d9deebfcac055face01dae3fc9de15 SHA512 15bc833e89839be89dfa35a23ae22ad0f9a19e8efd36211010c9f59e974de7c569576db36e26d6ab302543ff427604b5efb1b7badf62489a5e82a193ef155570
+DIST abyss-2.3.4.tar.gz 3511137 BLAKE2B 2b7449233055d22330f44951f9f6d5ff1a116fa3e19c09c17cd4fa517d2fc055c4f00ccb82c7e09b1b939ac6f7a1caf73cf73c33bd3c8aa9ff11879c227a2aaa SHA512 9d4e418399dd62883b53e831f51a0bd2ba228da73eda6c6459cd729c002eb0487f9613fca1c9bd0f4fbb076eed8a9b952505ee97143ab7dde537c23e4a246cd4
diff --git a/sci-biology/abyss/abyss-2.3.4.ebuild b/sci-biology/abyss/abyss-2.3.4.ebuild
new file mode 100644
index 000000000000..c2e1ffd29b32
--- /dev/null
+++ b/sci-biology/abyss/abyss-2.3.4.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
+HOMEPAGE="https://www.bcgsc.ca/resources/software/abyss/"
+SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="openmp misc-haskell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-cpp/sparsehash
+	dev-libs/boost:=
+	misc-haskell? (
+		dev-libs/gmp:0=
+		dev-libs/libffi:0=
+	)
+	sys-cluster/openmpi
+	dev-db/sqlite:3
+"
+DEPEND="${RDEPEND}
+	misc-haskell? (
+		dev-lang/ghc
+	)
+"
+
+# todo: --enable-maxk=N configure option
+# todo: also allow build with mpich (--enable-mpich)
+
+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) --enable-maxk=256
+}
-- 
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