From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (2048 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 4D6AD158087 for ; Thu, 13 Jan 2022 11:21:48 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 3B07F2BC00B; Thu, 13 Jan 2022 11:21:47 +0000 (UTC) Received: from smtp.gentoo.org (mail.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 835972BC00B for ; Thu, 13 Jan 2022 11:21:46 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id B471B34346C for ; Thu, 13 Jan 2022 11:21:44 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 1C62C21D for ; Thu, 13 Jan 2022 11:21:43 +0000 (UTC) From: "Andrew Ammerlaan" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Andrew Ammerlaan" Message-ID: <1642072896.03ada3844855dd1c9ff2627e7f9239d0248e7cc6.andrewammerlaan@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/abyss/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/abyss/Manifest sci-biology/abyss/abyss-2.3.4.ebuild X-VCS-Directories: sci-biology/abyss/ X-VCS-Committer: andrewammerlaan X-VCS-Committer-Name: Andrew Ammerlaan X-VCS-Revision: 03ada3844855dd1c9ff2627e7f9239d0248e7cc6 X-VCS-Branch: master Date: Thu, 13 Jan 2022 11:21:43 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 5cf414ae-d675-4f82-a91b-118bd375659a X-Archives-Hash: d4a00af98e4431741e1b71b184d986c9 commit: 03ada3844855dd1c9ff2627e7f9239d0248e7cc6 Author: Andrew Ammerlaan gentoo org> AuthorDate: Thu Jan 13 11:19:37 2022 +0000 Commit: Andrew Ammerlaan gentoo org> CommitDate: Thu Jan 13 11:21:36 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=03ada384 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 gentoo.org> sci-biology/abyss/Manifest | 1 + sci-biology/abyss/abyss-2.3.4.ebuild | 57 ++++++++++++++++++++++++++++++++++++ 2 files changed, 58 insertions(+) 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 +}