Date: Sun, 5 Mar 2023 00:18:30 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: a5b1448e8eb2 - main - biology/fastqc: Update to 0.12.1 Message-ID: <202303050018.3250IUa2054582@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=a5b1448e8eb2d2558dd94d007dba3a7b591b8b73 commit a5b1448e8eb2d2558dd94d007dba3a7b591b8b73 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2023-03-05 00:17:20 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> 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
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