From nobody Sun Mar 05 00:18:30 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 4PTj3p5kSSz3vhcm; Sun, 5 Mar 2023 00:18:30 +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 4PTj3p5Bvsz4NPD; Sun, 5 Mar 2023 00:18:30 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1677975510; 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=c5x21yvX13QrIRDflj0wChwvhw2CGdIgvsxEKzvbnZ8=; b=ok+g902S5bvQP5/yKpyXQ8OQCE3cCsLipa+wIWDO2fBFXFypDT5fHKIavsR0TDfw5FepOW cBr07P9r2/tShUj5z6EVU5uUs+BJhYYOS60ZYli1MojszYEnfG5NdgSbTvdettwE+otS1W /rRQg//0EX514JiglTxRlkULCKDO9iNbduLJjqtu5kAta6wySR2ej0tWgTskwGld/lCcBj FdqOuUxOBoLmfGACcHPXs6Ekz2qRaAXcuXGa0obHddZkyru8aTnbhOJZuWZ14m1ys3g6HR q1iAFBSyiv4SkmTC6frtjyfeKWWwqsOwBp8Ds/qeUBieHsQJlHpM8z3is/BnjA== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1677975510; 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=c5x21yvX13QrIRDflj0wChwvhw2CGdIgvsxEKzvbnZ8=; b=nGh9YmVWfuqu0HhmI/4gaiaYcyioBAkvowaxFi/8cAGR71nFVI1y4+uYGab9GYbrwp4mTK MsHw5hPxvCbKQ6jNYmMsBieFtIVmge7GJQHRQkwCEyXhfx2Uc1Pxf/HHe8PpCiMRQ9Iozl wJGbOPNwvwk8Zi4sglfSgWKGnJJ4VfkmRlovFVyYYRt8kP9qI+Sf8XYu49/KfrYCiNNU1z BMGYIiJwDYrE6kIYJbMsT5j6JI23rVhBNRAFUcSCzra3yYq6Ehsf3zDV+RyheqxWeO5aoz OAvltgmBFNHHypPLANIZdpx91UPFzytrbbY73CjPJKa+0GN2py5uu9G5+kuvfQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1677975510; a=rsa-sha256; cv=none; b=UPjNC8xtnC48eeemz/Fl3rHr++8zJVEix1z3JJSSLl5ILdUGuiucBQSdnOo8JmRUUrj7kd 7J8fxCMJRWljDclkfn+wF87+HxcirddKy8VJoCojT4WnFkiyiY0ZGNO9Y2hK3Ub8Whs8EG HiO4A0atJ4292messHX8Kpn0eBcTDfkn91nd3+kXAmZcBO8En2lePma556j26UuoNaLx+p UQBXRfVAgQbJNEHA4BC4THy55gjo017GD7VxfiO//tSj2JMfLGdmSpuCTermdBgSSKYUO/ gV/yKyTCfTBubr2ej6CffAGFN8NgOCBvLmv9JHpgmXxSM69VgD6bzwzP3FgxIw== 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 4PTj3p4FV3z10cq; Sun, 5 Mar 2023 00:18:30 +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 3250IUuO054583; Sun, 5 Mar 2023 00:18:30 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 3250IUa2054582; Sun, 5 Mar 2023 00:18:30 GMT (envelope-from git) Date: Sun, 5 Mar 2023 00:18:30 GMT Message-Id: <202303050018.3250IUa2054582@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: a5b1448e8eb2 - main - biology/fastqc: Update to 0.12.1 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: a5b1448e8eb2d2558dd94d007dba3a7b591b8b73 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=a5b1448e8eb2d2558dd94d007dba3a7b591b8b73 commit a5b1448e8eb2d2558dd94d007dba3a7b591b8b73 Author: Jason W. Bacon AuthorDate: 2023-03-05 00:17:20 +0000 Commit: Jason W. Bacon CommitDate: 2023-03-05 00:17:20 +0000 biology/fastqc: Update to 0.12.1 Several feature enhancements and a few bug fixes Changes: https://github.com/s-andrews/FastQC/releases Reported by: portscout --- biology/fastqc/Makefile | 2 +- biology/fastqc/distinfo | 6 +++--- biology/fastqc/pkg-plist | 44 +++++++++++++++++++++++++++++++++++++++++++- 3 files changed, 47 insertions(+), 5 deletions(-) diff --git a/biology/fastqc/Makefile b/biology/fastqc/Makefile index a6ffbc2eaf07..05f6306c7ec0 100644 --- a/biology/fastqc/Makefile +++ b/biology/fastqc/Makefile @@ -1,5 +1,5 @@ PORTNAME= fastqc -DISTVERSION= 0.11.9 +DISTVERSION= 0.12.1 CATEGORIES= biology java perl5 MASTER_SITES= https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ DISTNAME= ${PORTNAME}_v${DISTVERSIONPREFIX}${DISTVERSION} diff --git a/biology/fastqc/distinfo b/biology/fastqc/distinfo index 55c4a0629f50..230cfc1d46b2 100644 --- a/biology/fastqc/distinfo +++ b/biology/fastqc/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1612358925 -SHA256 (fastqc_v0.11.9.zip) = 15510a176ef798e40325b717cac556509fb218268cfdb9a35ea6776498321369 -SIZE (fastqc_v0.11.9.zip) = 10249221 +TIMESTAMP = 1677972229 +SHA256 (fastqc_v0.12.1.zip) = 5f4dba8780231a25a6b8e11ab2c238601920c9704caa5458d9de559575d58aa7 +SIZE (fastqc_v0.12.1.zip) = 11709692 diff --git a/biology/fastqc/pkg-plist b/biology/fastqc/pkg-plist index ffbb0338d11e..7ff0acbda930 100644 --- a/biology/fastqc/pkg-plist +++ b/biology/fastqc/pkg-plist @@ -2,10 +2,49 @@ bin/fastqc %%DATADIR%%/Configuration/adapter_list.txt %%DATADIR%%/Configuration/contaminant_list.txt %%DATADIR%%/Configuration/limits.txt +%%DATADIR%%/Help/1 Introduction/.svn/entries +%%DATADIR%%/Help/1 Introduction/.svn/text-base/1.1 What is FastQC.html.svn-base %%DATADIR%%/Help/1 Introduction/1.1 What is FastQC.html +%%DATADIR%%/Help/2 Basic Operations/.svn/entries +%%DATADIR%%/Help/2 Basic Operations/.svn/text-base/2.1 Opening a sequence file.html.svn-base +%%DATADIR%%/Help/2 Basic Operations/.svn/text-base/2.2 Evaluating Results.html.svn-base +%%DATADIR%%/Help/2 Basic Operations/.svn/text-base/2.3 Saving a Report.html.svn-base %%DATADIR%%/Help/2 Basic Operations/2.1 Opening a sequence file.html %%DATADIR%%/Help/2 Basic Operations/2.2 Evaluating Results.html %%DATADIR%%/Help/2 Basic Operations/2.3 Saving a Report.html +%%DATADIR%%/Help/3 Analysis Modules/.svn/entries +%%DATADIR%%/Help/3 Analysis Modules/.svn/prop-base/duplication_levels.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/prop-base/kmer_profiles.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/prop-base/per_base_gc_content.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/prop-base/per_base_n_content.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/prop-base/per_base_quality.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/prop-base/per_base_sequence_content.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/prop-base/per_sequence_gc_content.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/prop-base/per_sequence_quality.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/prop-base/per_tile_quality.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/prop-base/sequence_length_distribution.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/1 Basic Statistics.html.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/10 Adapter Content.html.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/11 Kmer Content.html.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/12 Per Tile Sequence Quality.html.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/2 Per Base Sequence Quality.html.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/3 Per Sequence Quality Scores.html.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/4 Per Base Sequence Content.html.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/5 Per Sequence GC Content.html.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/6 Per Base N Content.html.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/7 Sequence Length Distribution.html.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/8 Duplicate Sequences.html.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/9 Overrepresented Sequences.html.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/duplication_levels.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/kmer_profiles.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/per_base_gc_content.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/per_base_n_content.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/per_base_quality.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/per_base_sequence_content.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/per_sequence_gc_content.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/per_sequence_quality.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/per_tile_quality.png.svn-base +%%DATADIR%%/Help/3 Analysis Modules/.svn/text-base/sequence_length_distribution.png.svn-base %%DATADIR%%/Help/3 Analysis Modules/1 Basic Statistics.html %%DATADIR%%/Help/3 Analysis Modules/10 Adapter Content.html %%DATADIR%%/Help/3 Analysis Modules/11 Kmer Content.html @@ -35,6 +74,7 @@ bin/fastqc %%DATADIR%%/Templates/fastqc2fo.xsl %%DATADIR%%/Templates/header_template.html %%JAVAJARDIR%%/fastqc/cisd-jhdf5.jar +%%JAVAJARDIR%%/fastqc/htsjdk.jar %%JAVAJARDIR%%/fastqc/jbzip2-0.9.jar %%JAVAJARDIR%%/fastqc/net/sourceforge/iharder/base64/Base64$1.class %%JAVAJARDIR%%/fastqc/net/sourceforge/iharder/base64/Base64$InputStream.class @@ -116,7 +156,6 @@ bin/fastqc %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/util/MathUtils.class %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/util/Precision.class %%JAVAJARDIR%%/fastqc/org/apache/commons/math3/util/ResizableDoubleArray.class -%%JAVAJARDIR%%/fastqc/sam-1.103.jar %%JAVAJARDIR%%/fastqc/uk/ac/babraham/FastQC/Analysis/AnalysisListener.class %%JAVAJARDIR%%/fastqc/uk/ac/babraham/FastQC/Analysis/AnalysisQueue.class %%JAVAJARDIR%%/fastqc/uk/ac/babraham/FastQC/Analysis/AnalysisRunner.class @@ -198,6 +237,9 @@ bin/fastqc %%JAVAJARDIR%%/fastqc/uk/ac/babraham/FastQC/Statistics/PearsonCorrelation.class %%JAVAJARDIR%%/fastqc/uk/ac/babraham/FastQC/Utilities/CasavaBasename.class %%JAVAJARDIR%%/fastqc/uk/ac/babraham/FastQC/Utilities/HotColdColourGradient.class +%%JAVAJARDIR%%/fastqc/uk/ac/babraham/FastQC/Utilities/ImageSaver/SVGGenerator$SVGGraphics.class +%%JAVAJARDIR%%/fastqc/uk/ac/babraham/FastQC/Utilities/ImageSaver/SVGGenerator.class +%%JAVAJARDIR%%/fastqc/uk/ac/babraham/FastQC/Utilities/ImageSaver/SVGImageSaver.class %%JAVAJARDIR%%/fastqc/uk/ac/babraham/FastQC/Utilities/ImageToBase64.class %%JAVAJARDIR%%/fastqc/uk/ac/babraham/FastQC/Utilities/MultiMemberGZIPInputStream.class %%JAVAJARDIR%%/fastqc/uk/ac/babraham/FastQC/Utilities/NameFormatException.class