From nobody Thu Jan 05 23:21:38 2023 X-Original-To: dev-commits-ports-all@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 4Np2Xy6tZXz2qmGh; Thu, 5 Jan 2023 23:21:38 +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 "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Np2Xy6VFJz3syl; Thu, 5 Jan 2023 23:21:38 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1672960898; 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=a4W60VeefTibB+WPG3rHXehPLDWbOuWgHBxcKAlc0Po=; b=FwgCpGe8BAWPVcQv2ASjwjw2ebomHpnuEU+Jt3A/5kRz6serqujjRwlWd+qMh9LyRp7dv5 OTId0dkGr3iNLUMojgv6+SZBKeqJjwYv9QbAcWBDEVeo3OqQw4Ib+Fq9hcfmX9DHhwl30K vigmam3+nD1M4MgLZNQ2uQ0uDrcvPe0b1/xduPXSqm9T/c8dsr59fHPU6VvcFEc4F1VMS9 2bnQcIeR3fbjlBf7OimGmhhSD2SlFobtYWDqd75ZS3zvtNjb171TrXm43PdQMBVFb2lOYw aMMZImCHnNIP2fkYC8+xL4EixifvN5IshgIrTSF7fs306CteHKhExUxZzMQj+g== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1672960898; 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=a4W60VeefTibB+WPG3rHXehPLDWbOuWgHBxcKAlc0Po=; b=lOwTAYYQyihST7rBB7Mp1YPmR7M83Fyxv611sSroCqFEQQOtyuQrDCwzKclYFKd+x5bLnu bP8u1fCEtSub5CZjt17Ise5qgEj+E3SAAH9H+iEGbajWiiJpyBHTPb7Ernw7hzoqnhSRvs wVxTHhQKuUvkVKj2Ykn58GsrJt2vM4i0q/4Pf1EVZm6dpc3hqZa/+UEKFCJUFIzS68g3X0 cYIrYAGTtCxDKxPMUzp0Ibd431dqrg7W97eI6Tss1UWdCVEAZEMpvmsVqZTmii2thukB1B BdaCL5N+v1K9+nrzQtC1HsapszGKNOe6g4+gXqvyDWezwicuIJvnLdXh8hP0vg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1672960898; a=rsa-sha256; cv=none; b=biSTc3A8hQbz7c1H8WqZIw727wenojrXJI3EdJjUxxe6qjKIRZMibgsLNTdZcF+4oYKR7l vaHZfMTngzLN/gpPPiFQzN5fYoer/vdD3twTwSAzIk3pMg/T34wQoV2G036EV6L75t1mWb q4PqNxkZ/FwlPUE46GerefcmkZnWpXCimwWzu5xLLTsXMBmQtWT4lspC+/IvRbTHOKoUZq OE5W7KUrhRqGdCgAuEXhmoMLk6Fbrl25Y2gJsPAOS1IihPRqC5j5agOR5LdT6wvh7wdV35 7pB+4a4GJZVDc9B+L9XWkCqUZ8aCb4BGUPZhdgfQB6wdo3I8tc+rDRKsFvjGHw== 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 4Np2Xy5Z36z185G; Thu, 5 Jan 2023 23:21:38 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 305NLcwQ004689; Thu, 5 Jan 2023 23:21:38 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 305NLcBJ004688; Thu, 5 Jan 2023 23:21:38 GMT (envelope-from git) Date: Thu, 5 Jan 2023 23:21:38 GMT Message-Id: <202301052321.305NLcBJ004688@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: 09c70c748898 - main - biology/bio-mocha: Update to 1.16 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@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: 09c70c7488989b1a37f4da6a447871c5bea06ee0 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=09c70c7488989b1a37f4da6a447871c5bea06ee0 commit 09c70c7488989b1a37f4da6a447871c5bea06ee0 Author: Jason W. Bacon AuthorDate: 2023-01-05 23:21:03 +0000 Commit: Jason W. Bacon CommitDate: 2023-01-05 23:21:03 +0000 biology/bio-mocha: Update to 1.16 New release to sync with bcftools Changes: https://github.com/freeseek/mocha/commits/master --- biology/bio-mocha/Makefile | 10 ++++------ biology/bio-mocha/distinfo | 10 +++++----- biology/bio-mocha/pkg-plist | 2 -- 3 files changed, 9 insertions(+), 13 deletions(-) diff --git a/biology/bio-mocha/Makefile b/biology/bio-mocha/Makefile index fb552c0676e7..33147346e72d 100644 --- a/biology/bio-mocha/Makefile +++ b/biology/bio-mocha/Makefile @@ -1,9 +1,8 @@ PORTNAME= bio-mocha -DISTVERSION= 1.14 -PORTREVISION= 1 +DISTVERSION= 1.16 CATEGORIES= biology MASTER_SITES= https://software.broadinstitute.org/software/mocha/ -DISTFILES+= ${PORTNAME}_${DISTVERSION}-20220112.tar.gz +DISTFILES+= ${PORTNAME}_${DISTVERSION}-20221221.tar.gz MAINTAINER= jwb@FreeBSD.org COMMENT= Bcftools plugin for mosaic chromosomal alteration analysis @@ -21,7 +20,7 @@ USE_PERL5= test GH_ACCOUNT= samtools GH_PROJECT= bcftools -GH_TAGNAME= 1.15 +GH_TAGNAME= 1.16 GNU_CONFIGURE= yes SHEBANG_FILES= misc/* test/test.pl @@ -34,6 +33,7 @@ pre-configure: @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \ ${WRKSRC}/configure.ac +# One .so for each .c in the mocha distfile do-install: ${MKDIR} ${STAGEDIR}${PREFIX}/libexec/bcftools ${INSTALL_PROGRAM} ${WRKSRC}/plugins/extendFMT.so \ @@ -42,8 +42,6 @@ do-install: ${STAGEDIR}${PREFIX}/libexec/bcftools ${INSTALL_PROGRAM} ${WRKSRC}/plugins/mochatools.so \ ${STAGEDIR}${PREFIX}/libexec/bcftools - ${INSTALL_PROGRAM} ${WRKSRC}/plugins/score.so \ - ${STAGEDIR}${PREFIX}/libexec/bcftools ${INSTALL_PROGRAM} ${WRKSRC}/plugins/trio-phase.so \ ${STAGEDIR}${PREFIX}/libexec/bcftools (cd ${WRKSRC}/MoCha && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}) diff --git a/biology/bio-mocha/distinfo b/biology/bio-mocha/distinfo index 6f18a06e9fb5..c5a05127a3d6 100644 --- a/biology/bio-mocha/distinfo +++ b/biology/bio-mocha/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1645832006 -SHA256 (bio-mocha_1.14-20220112.tar.gz) = 189a522418f12cbb04e6c5ccae130dbae1682907808f4cb594af4ff386651068 -SIZE (bio-mocha_1.14-20220112.tar.gz) = 75910 -SHA256 (samtools-bcftools-1.14-1.15_GH0.tar.gz) = 6b263270c62b156d2604150ca7e64b06a80282e049759b2668de24cbce1b1946 -SIZE (samtools-bcftools-1.14-1.15_GH0.tar.gz) = 3347901 +TIMESTAMP = 1672095342 +SHA256 (bio-mocha_1.16-20221221.tar.gz) = 576cbdda53760f353fc8fd989751716b1d4f8c5e1921f838c263476282cced86 +SIZE (bio-mocha_1.16-20221221.tar.gz) = 68625 +SHA256 (samtools-bcftools-1.16_GH0.tar.gz) = c44c85a04e058e1f1eceeb712106031100bbd700b8ff3f623f7ff872469a4ba3 +SIZE (samtools-bcftools-1.16_GH0.tar.gz) = 3432435 diff --git a/biology/bio-mocha/pkg-plist b/biology/bio-mocha/pkg-plist index 4604936e8e0f..a56018707fc6 100644 --- a/biology/bio-mocha/pkg-plist +++ b/biology/bio-mocha/pkg-plist @@ -1,9 +1,7 @@ libexec/bcftools/extendFMT.so libexec/bcftools/mocha.so libexec/bcftools/mochatools.so -libexec/bcftools/score.so libexec/bcftools/trio-phase.so -%%DATADIR%%/assoc_plot.R %%DATADIR%%/mocha_plot.R %%DATADIR%%/pileup_plot.R %%DATADIR%%/summary_plot.R