diff options
author | bacon <bacon@pkgsrc.org> | 2021-01-20 15:57:17 +0000 |
---|---|---|
committer | bacon <bacon@pkgsrc.org> | 2021-01-20 15:57:17 +0000 |
commit | 97a3ac93fdffde16c7c04fd51682661419900483 (patch) | |
tree | e95aea94a6bca0dc95d1603dad8db0d5c45daebb /biology | |
parent | 8fd0180a5915f4fb689f6b5ab3d811b8e3b9e77e (diff) | |
download | pkgsrc-97a3ac93fdffde16c7c04fd51682661419900483.tar.gz |
biology/fastqc: import fastqc-0.11.9
FastQC aims to provide a simple way to do some quality control checks on raw
sequence data coming from high throughput sequencing pipelines. It provides a
modular set of analyses which you can use to give a quick impression of whether
your data has any problems of which you should be aware before doing any
further analysis.
Diffstat (limited to 'biology')
-rw-r--r-- | biology/fastqc/DESCR | 5 | ||||
-rw-r--r-- | biology/fastqc/Makefile | 44 | ||||
-rw-r--r-- | biology/fastqc/PLIST | 246 | ||||
-rw-r--r-- | biology/fastqc/distinfo | 6 |
4 files changed, 301 insertions, 0 deletions
diff --git a/biology/fastqc/DESCR b/biology/fastqc/DESCR new file mode 100644 index 00000000000..63c71afebdc --- /dev/null +++ b/biology/fastqc/DESCR @@ -0,0 +1,5 @@ +FastQC aims to provide a simple way to do some quality control checks on raw +sequence data coming from high throughput sequencing pipelines. It provides a +modular set of analyses which you can use to give a quick impression of whether +your data has any problems of which you should be aware before doing any +further analysis. diff --git a/biology/fastqc/Makefile b/biology/fastqc/Makefile new file mode 100644 index 00000000000..0f7949a3a2e --- /dev/null +++ b/biology/fastqc/Makefile @@ -0,0 +1,44 @@ +# $NetBSD: Makefile,v 1.1 2021/01/20 15:57:17 bacon Exp $ + +DISTNAME= fastqc_v${PKGVERSION_NOREV} +PKGNAME= fastqc-0.11.9 +CATEGORIES= biology +MASTER_SITES= https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ +EXTRACT_SUFX= .zip + +MAINTAINER= bacon@NetBSD.org +HOMEPAGE= https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ +COMMENT= Quality control tool for high throughput sequence data +LICENSE= gnu-gpl-v3 + +SUBST_CLASSES+= javapath +SUBST_STAGE.javapath= pre-configure +SUBST_SED.javapath+= -e 's|$$RealBin$$delimiter|${DATADIR}$$delimiter${JAVAJARDIR}/fastqc$$delimiter|g' +SUBST_SED.javapath+= -e 's|$$RealBin/|${JAVAJARDIR}/fastqc/|g' +SUBST_FILES.javapath+= fastqc + +USE_TOOLS+= perl:run pax +USE_JAVA= run +USE_JAVA2= 8 + +WRKSRC= ${WRKDIR}/FastQC +REPLACE_PERL= fastqc +NO_BUILD= yes + +DATADIR= ${PREFIX}/share/fastqc +DOCSDIR= ${PREFIX}/share/doc/fastqc +JAVAJARDIR= ${PREFIX}/share/java/classes + +INSTALLATION_DIRS= bin ${DATADIR} ${DOCSDIR} ${JAVAJARDIR}/fastqc + +do-install: + ${INSTALL_DATA} ${WRKSRC}/*.jar ${DESTDIR}${JAVAJARDIR}/fastqc + ${INSTALL_SCRIPT} ${WRKSRC}/fastqc ${DESTDIR}${PREFIX}/bin + cd ${WRKSRC} && pax -rw Configuration ${DESTDIR}${DATADIR} + cd ${WRKSRC} && pax -rw Templates ${DESTDIR}${DATADIR} + cd ${WRKSRC} && pax -rw net ${DESTDIR}${JAVAJARDIR}/fastqc + cd ${WRKSRC} && pax -rw org ${DESTDIR}${JAVAJARDIR}/fastqc + cd ${WRKSRC} && pax -rw uk ${DESTDIR}${JAVAJARDIR}/fastqc + cd ${WRKSRC} && pax -rw Help ${DESTDIR}${DOCSDIR} + +.include "../../mk/bsd.pkg.mk" diff --git a/biology/fastqc/PLIST b/biology/fastqc/PLIST new file mode 100644 index 00000000000..c6ba4bc16b2 --- /dev/null +++ b/biology/fastqc/PLIST @@ -0,0 +1,246 @@ +@comment $NetBSD: PLIST,v 1.1 2021/01/20 15:57:17 bacon Exp $ +bin/fastqc +share/doc/fastqc/Help/1 Introduction/.svn/entries +share/doc/fastqc/Help/1 Introduction/.svn/text-base/1.1 What is FastQC.html.svn-base +share/doc/fastqc/Help/1 Introduction/1.1 What is FastQC.html +share/doc/fastqc/Help/2 Basic Operations/.svn/entries +share/doc/fastqc/Help/2 Basic Operations/.svn/text-base/2.1 Opening a sequence file.html.svn-base +share/doc/fastqc/Help/2 Basic Operations/.svn/text-base/2.2 Evaluating Results.html.svn-base +share/doc/fastqc/Help/2 Basic Operations/.svn/text-base/2.3 Saving a Report.html.svn-base +share/doc/fastqc/Help/2 Basic Operations/2.1 Opening a sequence file.html +share/doc/fastqc/Help/2 Basic Operations/2.2 Evaluating Results.html +share/doc/fastqc/Help/2 Basic Operations/2.3 Saving a Report.html +share/doc/fastqc/Help/3 Analysis Modules/.svn/entries +share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/duplication_levels.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/kmer_profiles.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_base_gc_content.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_base_n_content.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_base_quality.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_base_sequence_content.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_sequence_gc_content.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_sequence_quality.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/per_tile_quality.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/prop-base/sequence_length_distribution.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/1 Basic Statistics.html.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/10 Adapter Content.html.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/11 Kmer Content.html.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/12 Per Tile Sequence Quality.html.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/2 Per Base Sequence Quality.html.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/3 Per Sequence Quality Scores.html.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/4 Per Base Sequence Content.html.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/5 Per Sequence GC Content.html.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/6 Per Base N Content.html.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/7 Sequence Length Distribution.html.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/8 Duplicate Sequences.html.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/9 Overrepresented Sequences.html.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/duplication_levels.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/kmer_profiles.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_base_gc_content.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_base_n_content.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_base_quality.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_base_sequence_content.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_sequence_gc_content.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_sequence_quality.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/per_tile_quality.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/.svn/text-base/sequence_length_distribution.png.svn-base +share/doc/fastqc/Help/3 Analysis Modules/1 Basic Statistics.html +share/doc/fastqc/Help/3 Analysis Modules/10 Adapter Content.html +share/doc/fastqc/Help/3 Analysis Modules/11 Kmer Content.html +share/doc/fastqc/Help/3 Analysis Modules/12 Per Tile Sequence Quality.html +share/doc/fastqc/Help/3 Analysis Modules/2 Per Base Sequence Quality.html +share/doc/fastqc/Help/3 Analysis Modules/3 Per Sequence Quality Scores.html +share/doc/fastqc/Help/3 Analysis Modules/4 Per Base Sequence Content.html +share/doc/fastqc/Help/3 Analysis Modules/5 Per Sequence GC Content.html +share/doc/fastqc/Help/3 Analysis Modules/6 Per Base N Content.html +share/doc/fastqc/Help/3 Analysis Modules/7 Sequence Length Distribution.html +share/doc/fastqc/Help/3 Analysis Modules/8 Duplicate Sequences.html +share/doc/fastqc/Help/3 Analysis Modules/9 Overrepresented Sequences.html +share/doc/fastqc/Help/3 Analysis Modules/duplication_levels.png +share/doc/fastqc/Help/3 Analysis Modules/kmer_profiles.png +share/doc/fastqc/Help/3 Analysis Modules/per_base_gc_content.png +share/doc/fastqc/Help/3 Analysis Modules/per_base_n_content.png +share/doc/fastqc/Help/3 Analysis Modules/per_base_quality.png +share/doc/fastqc/Help/3 Analysis Modules/per_base_sequence_content.png +share/doc/fastqc/Help/3 Analysis Modules/per_sequence_gc_content.png +share/doc/fastqc/Help/3 Analysis Modules/per_sequence_quality.png +share/doc/fastqc/Help/3 Analysis Modules/per_tile_quality.png +share/doc/fastqc/Help/3 Analysis Modules/sequence_length_distribution.png +share/fastqc/Configuration/adapter_list.txt +share/fastqc/Configuration/contaminant_list.txt +share/fastqc/Configuration/limits.txt +share/fastqc/Templates/Icons/error.png +share/fastqc/Templates/Icons/fastqc_icon.png +share/fastqc/Templates/Icons/tick.png +share/fastqc/Templates/Icons/warning.png +share/fastqc/Templates/fastqc2fo.xsl +share/fastqc/Templates/header_template.html +share/java/classes/fastqc/cisd-jhdf5.jar +share/java/classes/fastqc/jbzip2-0.9.jar +share/java/classes/fastqc/net/sourceforge/iharder/base64/Base64$1.class +share/java/classes/fastqc/net/sourceforge/iharder/base64/Base64$InputStream.class +share/java/classes/fastqc/net/sourceforge/iharder/base64/Base64$OutputStream.class +share/java/classes/fastqc/net/sourceforge/iharder/base64/Base64.class +share/java/classes/fastqc/org/apache/commons/math3/analysis/UnivariateFunction.class +share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/AbstractUnivariateSolver.class +share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/AllowedSolution.class +share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/BaseAbstractUnivariateSolver.class +share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/BaseUnivariateSolver.class +share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/BracketedUnivariateSolver.class +share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/BrentSolver.class +share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/UnivariateSolver.class +share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/UnivariateSolverUtils.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/AbstractIntegerDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/AbstractRealDistribution$1.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/AbstractRealDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/BetaDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/BinomialDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/CauchyDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/ChiSquaredDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/FDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/GammaDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/HypergeometricDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/IntegerDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/NormalDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/PascalDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/PoissonDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/RealDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/SaddlePointExpansion.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/TDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/WeibullDistribution.class +share/java/classes/fastqc/org/apache/commons/math3/distribution/ZipfDistribution.class 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+share/java/classes/fastqc/uk/ac/babraham/FastQC/Report/HTMLReportArchive.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Report/stylesheet.txt +share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/error.png +share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/fastqc_icon.png +share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/fastqc_icon.svg +share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/fastqc_icon_100.png +share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/tick.png +share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/warning.png +share/java/classes/fastqc/uk/ac/babraham/FastQC/Results/ResultsPanel$ModuleRenderer.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Results/ResultsPanel.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/BAMFile.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Contaminant/Contaminant.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminantHit.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/FastQFile.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/QualityEncoding/PhredEncoding.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Sequence.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFactory.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFile.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFileGroup.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFormatException.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Statistics/NormalDistribution.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Statistics/PearsonCorrelation.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/CasavaBasename.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/HotColdColourGradient.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/ImageToBase64.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/MultiMemberGZIPInputStream.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/NameFormatException.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/NanoporeBasename.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/QualityCount.class +share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/RGB.class diff --git a/biology/fastqc/distinfo b/biology/fastqc/distinfo new file mode 100644 index 00000000000..cfde8fef2ee --- /dev/null +++ b/biology/fastqc/distinfo @@ -0,0 +1,6 @@ +$NetBSD: distinfo,v 1.1 2021/01/20 15:57:17 bacon Exp $ + +SHA1 (fastqc_v0.11.9.zip) = 077003dcef8933c4b43ac5b6945fdc31b53f746c +RMD160 (fastqc_v0.11.9.zip) = 9c06aff0044e0f8b4866ae9c731543017e71b9e0 +SHA512 (fastqc_v0.11.9.zip) = f9ed1546d08e941abcca8ff507d2cf2d455831fcb3d36def7d9881f4f23c4d7874b62d28c5f9901149e1b5bc7ca5fe746c5a522785b7fe72bc9e96330b568bed +Size (fastqc_v0.11.9.zip) = 10249221 bytes |