From nobody Fri Jan 17 22:39:35 2025 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4YZZRW2mBmz5kLgB; Fri, 17 Jan 2025 22:39:35 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (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 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4YZZRW23qzz3Dgh; Fri, 17 Jan 2025 22:39:35 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1737153575; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=S/iihSeR1Zdv5SPVZF3CwT06o8qyk+g74Rd7w1QreZs=; b=I+x62YLKJLdSFrbq/uSmix1o7kYEBQ0L6XNQW0D6g4DSLWAqoMOQXOneYGqYbN6s84f7nc 2zNW8pryxu6gco+Wub854lGQH9Cy6NYoJiCt/ibKCvaGfQZ9oPf+93ytDuIgIJrD4Yu17v dRWQv9K4T3yTAvXsC5rhpYLGJuTeI57pMukIaJC8bpTE5h+pb4V5Wm0GswIcg5qnsHvx9U DhtI89Dwmgn/ziEQ7zIZH/gPzLswTBmMJf7gcTd61zYfmE3xBAQ/v4vTDV/SqQn07LvISp NNdVkvgCETgJ00mLCbeIg+VXq49lD9zv1QMm4BDfGvWlKz4SOEZ3DWRgYb0bbg== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1737153575; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=S/iihSeR1Zdv5SPVZF3CwT06o8qyk+g74Rd7w1QreZs=; b=w35p1e06c5ZGeSSHKS8vx+DPbQgsd5Gq9At3J5cn6Fhv5tCtuBVvkxMFKC0vYsYYIJF0U5 DIUeavKKPJoV+G0GlJ4ZSUnEWBM4yGbuLAo3w1Y9uScTDk+aeJ+0mxZjvf4kfNNNyBFl7v Ti1WNBGyLzqv/vzuBr8suCi+zkzlUreeIke75WsMwPMm/kiXV46zcfgEYeJlA21Xw3oOQG QmzuBtvcVrgL3vRd8eRSkbk6bVg4IdZCZsE+XCaJP8OyIjU2sm9lMI6aA4HwrlQtKLuDj7 AKQJz54CG+5SfgpcExfzz6mhh4vHmZDPQbqDKcCSKPiO19JZ0lPSJQLtKbXO6A== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1737153575; a=rsa-sha256; cv=none; b=WEoVHXsuueASgztsQvFLWL4BhUdlNltpD7EdiSZAVH5l3Tp5HcuU5Apsox88MkagU9tgZG urLyynw3TH//6XQBMCHccoMW97O4g/j83Vk3rgQ6iGw/7huc3E0cyJpOdKDqz2sQV5MS8X A2Vp6mSXdn+bc59MTJL1OXotEoRxhMf5ufMKGMc8IaiZSsaIO7gpDX0gqGCGLMzFqlxdxM fAr1y/XdDqnyXcpeWmgjGpAtqvM1+BJuItYY6sPeJF02phAWimAxi3Cg45SbaLUaGifuA7 YvIWx9wamUhxJWp6xKidzthSzaSqaLtkCS3JT5UJSOeh2OVbV1rUXK0vfiuFfw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (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) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4YZZRW1V9RzdL6; Fri, 17 Jan 2025 22:39:35 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 50HMdZG2047286; Fri, 17 Jan 2025 22:39:35 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 50HMdZCD047283; Fri, 17 Jan 2025 22:39:35 GMT (envelope-from git) Date: Fri, 17 Jan 2025 22:39:35 GMT Message-Id: <202501172239.50HMdZCD047283@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: e3e3bee19927 - main - biology/stacks: Update to 2.68 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: e3e3bee19927174745e10cb4188bec6c9b527fae Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=e3e3bee19927174745e10cb4188bec6c9b527fae commit e3e3bee19927174745e10cb4188bec6c9b527fae Author: Jason W. Bacon AuthorDate: 2025-01-17 22:38:18 +0000 Commit: Jason W. Bacon CommitDate: 2025-01-17 22:38:18 +0000 biology/stacks: Update to 2.68 Numerous fixes and improvements since 2.4 Changes: http://catchenlab.life.illinois.edu/stacks/changelog.php PR: 283257 Reported by: alster@vinterdalen.se --- biology/stacks/Makefile | 18 +++++------------- biology/stacks/distinfo | 6 +++--- biology/stacks/pkg-plist | 6 ++++-- 3 files changed, 12 insertions(+), 18 deletions(-) diff --git a/biology/stacks/Makefile b/biology/stacks/Makefile index b4301eec2bb7..5e1b270e1b98 100644 --- a/biology/stacks/Makefile +++ b/biology/stacks/Makefile @@ -1,8 +1,7 @@ PORTNAME= stacks -DISTVERSION= 2.4 -PORTREVISION= 2 +DISTVERSION= 2.68 CATEGORIES= biology perl5 python -MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/ +MASTER_SITES= https://catchenlab.life.illinois.edu/stacks/source/ MAINTAINER= jwb@FreeBSD.org COMMENT= Software pipeline for building loci from short-read sequences @@ -13,17 +12,10 @@ LICENSE_FILE= ${WRKSRC}/LICENSE USES= compiler:c++11-lang gmake python shebangfix -SHEBANG_FILES= scripts/*.pl scripts/*.py \ - scripts/stacks-integrate-alignments scripts/stacks-gdb +SHEBANG_FILES= scripts/* + GNU_CONFIGURE= yes LDFLAGS+= -lpthread -.include - -# Temp workaround, see PR 230888 -.if ${ARCH} == i386 -USE_GCC= yes -.endif - -.include +.include diff --git a/biology/stacks/distinfo b/biology/stacks/distinfo index 312ef425ec9d..ce462d89a52e 100644 --- a/biology/stacks/distinfo +++ b/biology/stacks/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1557519159 -SHA256 (stacks-2.4.tar.gz) = 30093d688a2dc62a19ea42a58065f024c8279419439049bcde186703e75641c1 -SIZE (stacks-2.4.tar.gz) = 10930616 +TIMESTAMP = 1733920483 +SHA256 (stacks-2.68.tar.gz) = 9dc51ea356d60eb4557b0b2d1a8854aafae492aed87f974e0249cc09aa5e7650 +SIZE (stacks-2.68.tar.gz) = 15552836 diff --git a/biology/stacks/pkg-plist b/biology/stacks/pkg-plist index 605cf4a295db..e3ca8c4a9b60 100644 --- a/biology/stacks/pkg-plist +++ b/biology/stacks/pkg-plist @@ -1,9 +1,7 @@ bin/clone_filter -bin/count_fixed_catalog_snps.py bin/cstacks bin/denovo_map.pl bin/gstacks -bin/integrate_alignments.py bin/kmer_filter bin/phasedstacks bin/populations @@ -11,8 +9,12 @@ bin/process_radtags bin/process_shortreads bin/ref_map.pl bin/sstacks +bin/stacks-count-reads-per-sample-per-locus bin/stacks-dist-extract bin/stacks-gdb +bin/stacks-hist2d-loci-samples-coverage bin/stacks-integrate-alignments +bin/stacks-private-alleles +bin/stacks-samtools-tview bin/tsv2bam bin/ustacks