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biology/fastqc: Update to 0.12.1
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Several feature enhancements and a few bug fixes
Changes: https://github.com/s-andrews/FastQC/releases

Reported by:    portscout
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Jason W. Bacon authored and Jason W. Bacon committed Mar 5, 2023
1 parent 330adfc commit a5b1448
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Showing 3 changed files with 47 additions and 5 deletions.
2 changes: 1 addition & 1 deletion biology/fastqc/Makefile
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@@ -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}
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6 changes: 3 additions & 3 deletions biology/fastqc/distinfo
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@@ -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
44 changes: 43 additions & 1 deletion biology/fastqc/pkg-plist
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Expand Up @@ -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
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%%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
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%%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
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%%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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