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Add fastqc: Quality control tool for high throughput sequence data
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By: outpaddling
Date: Fri Nov 3 16:18:34 2017 -0500
Changeset: d19e508e838919f58ccc73f0c923ea98e7a8f9b5
Modified Files:
Makefile
Added Files:
fastqc/DESCR
fastqc/Makefile
fastqc/PLIST
fastqc/TODO
fastqc/distinfo
Log Message:
Add fastqc: Quality control tool for high throughput sequence data
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d19e508e838919f58ccc73f0c923ea98e7a8f9b5
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
fastqc/DESCR | 5 +++
fastqc/Makefile | 53 +++++++++++++++++++++++
fastqc/PLIST | 127 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
fastqc/TODO | 1 +
fastqc/distinfo | 6 +++
6 files changed, 193 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index 2daae077c7..e7f118f11c 100644
--- a/Makefile
+++ b/Makefile
@@ -748,6 +748,7 @@ SUBDIR+= fastaunique
SUBDIR+= fastbit
SUBDIR+= fastjet
SUBDIR+= fastool
+SUBDIR+= fastqc
SUBDIR+= fastrpc
SUBDIR+= fbida
SUBDIR+= fbpager
diff --git a/fastqc/DESCR b/fastqc/DESCR
new file mode 100644
index 0000000000..63c71afebd
--- /dev/null
+++ b/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/fastqc/Makefile b/fastqc/Makefile
new file mode 100644
index 0000000000..1c456d74fd
--- /dev/null
+++ b/fastqc/Makefile
@@ -0,0 +1,53 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+# Fri Nov 3 16:02:27 CDT 2017 #
+###########################################################
+
+DISTNAME= fastqc_v${PORTVERSION}
+PKGNAME= fastqc-${PORTVERSION}
+CATEGORIES= biology
+MASTER_SITES= http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+EXTRACT_SUFX= .zip
+
+MAINTAINER= bacon4000%gmail.com@localhost
+HOMEPAGE= http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+COMMENT= Quality control tool for high throughput sequence data
+# Check this
+LICENSE= gnu-gpl-v3
+
+SUBST_CLASSES+= javapath
+SUBST_STAGE.javapath= post-patch
+SUBST_SED.javapath+= -e 's|$$RealBin$$delimiter|${JAVAJARDIR}$$delimiter|g'
+SUBST_SED.javapath+= -e 's|$$RealBin/|${JAVAJARDIR}/|g'
+SUBST_FILES.javapath+= ${WRKSRC}/fastqc
+
+USE_TOOLS+= perl:run pax
+REPLACE_PERL= fastqc
+NO_BUILD= yes
+
+WRKSRC= ${WRKDIR}/FastQC
+
+PORTVERSION= 0.11.5
+DATADIR= ${PREFIX}/share/fastqc
+DOCSDIR= ${PREFIX}/share/doc/fastqc
+USE_JAVA= yes
+JAVAJARDIR= ${PREFIX}/share/java/classes
+
+INSTALLATION_DIRS= bin ${DATADIR} ${DOCSDIR} ${JAVAJARDIR}
+
+do-install:
+ ${INSTALL_DATA} ${WRKSRC}/*.jar ${DESTDIR}${JAVAJARDIR}
+ ${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 uk \
+ ${DESTDIR}${JAVAJARDIR}
+ cd ${WRKSRC} && pax -rw 'Help' \
+ ${DESTDIR}${DOCSDIR}
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/fastqc/PLIST b/fastqc/PLIST
new file mode 100644
index 0000000000..0da02df4a7
--- /dev/null
+++ b/fastqc/PLIST
@@ -0,0 +1,127 @@
+@comment $NetBSD$
+bin/fastqc
+share/doc/fastqc/Help/1 Introduction/1.1 What is FastQC.html
+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/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/cisd-jhdf5.jar
+share/java/classes/jbzip2-0.9.jar
+share/java/classes/sam-1.103.jar
+share/java/classes/uk/ac/babraham/FastQC/Analysis/AnalysisListener.class
+share/java/classes/uk/ac/babraham/FastQC/Analysis/AnalysisQueue.class
+share/java/classes/uk/ac/babraham/FastQC/Analysis/AnalysisRunner.class
+share/java/classes/uk/ac/babraham/FastQC/Analysis/OfflineRunner.class
+share/java/classes/uk/ac/babraham/FastQC/Dialogs/AboutDialog$1.class
+share/java/classes/uk/ac/babraham/FastQC/Dialogs/AboutDialog.class
+share/java/classes/uk/ac/babraham/FastQC/Dialogs/FastQCTitlePanel$SmoothJLabel.class
+share/java/classes/uk/ac/babraham/FastQC/Dialogs/FastQCTitlePanel.class
+share/java/classes/uk/ac/babraham/FastQC/Dialogs/WelcomePanel.class
+share/java/classes/uk/ac/babraham/FastQC/FastQCApplication$1.class
+share/java/classes/uk/ac/babraham/FastQC/FastQCApplication.class
+share/java/classes/uk/ac/babraham/FastQC/FastQCConfig.class
+share/java/classes/uk/ac/babraham/FastQC/FastQCMenuBar.class
+share/java/classes/uk/ac/babraham/FastQC/FileFilters/BAMFileFilter.class
+share/java/classes/uk/ac/babraham/FastQC/FileFilters/CasavaFastQFileFilter.class
+share/java/classes/uk/ac/babraham/FastQC/FileFilters/FastQFileFilter.class
+share/java/classes/uk/ac/babraham/FastQC/FileFilters/GobyFileFilter.class
+share/java/classes/uk/ac/babraham/FastQC/FileFilters/MappedBAMFileFilter.class
+share/java/classes/uk/ac/babraham/FastQC/FileFilters/SequenceFileFilter.class
+share/java/classes/uk/ac/babraham/FastQC/Graphs/BaseGroup.class
+share/java/classes/uk/ac/babraham/FastQC/Graphs/LineGraph.class
+share/java/classes/uk/ac/babraham/FastQC/Graphs/QualityBoxPlot.class
+share/java/classes/uk/ac/babraham/FastQC/Graphs/TileGraph.class
+share/java/classes/uk/ac/babraham/FastQC/Help/HelpDialog.class
+share/java/classes/uk/ac/babraham/FastQC/Help/HelpIndexRoot$FileSorter.class
+share/java/classes/uk/ac/babraham/FastQC/Help/HelpIndexRoot.class
+share/java/classes/uk/ac/babraham/FastQC/Help/HelpPage.class
+share/java/classes/uk/ac/babraham/FastQC/Help/HelpPageDisplay$HelpEditor.class
+share/java/classes/uk/ac/babraham/FastQC/Help/HelpPageDisplay.class
+share/java/classes/uk/ac/babraham/FastQC/Help/HelpSearchPanel.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/AbstractQCModule.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/AdapterContent$Adapter.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/AdapterContent$ResultsTable.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/AdapterContent.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/BasicStats$ResultsTable.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/BasicStats.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/DuplicationLevel.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/GCModel/GCModel.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/GCModel/GCModelValue.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/KmerContent$Kmer.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/KmerContent$ResultsTable.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/KmerContent.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/ModuleConfig.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/ModuleFactory.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/NContent.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs$OverrepresentedSeq.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs$ResultsTable.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/PerBaseQualityScores.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/PerBaseSequenceContent.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/PerSequenceGCContent.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/PerSequenceQualityScores.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/PerTileQualityScores.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/QCModule.class
+share/java/classes/uk/ac/babraham/FastQC/Modules/SequenceLengthDistribution.class
+share/java/classes/uk/ac/babraham/FastQC/Report/HTMLReportArchive.class
+share/java/classes/uk/ac/babraham/FastQC/Report/stylesheet.txt
+share/java/classes/uk/ac/babraham/FastQC/Resources/error.png
+share/java/classes/uk/ac/babraham/FastQC/Resources/fastqc_icon.png
+share/java/classes/uk/ac/babraham/FastQC/Resources/fastqc_icon.svg
+share/java/classes/uk/ac/babraham/FastQC/Resources/fastqc_icon_100.png
+share/java/classes/uk/ac/babraham/FastQC/Resources/tick.png
+share/java/classes/uk/ac/babraham/FastQC/Resources/warning.png
+share/java/classes/uk/ac/babraham/FastQC/Results/ResultsPanel$ModuleRenderer.class
+share/java/classes/uk/ac/babraham/FastQC/Results/ResultsPanel.class
+share/java/classes/uk/ac/babraham/FastQC/Sequence/BAMFile.class
+share/java/classes/uk/ac/babraham/FastQC/Sequence/Contaminant/Contaminant.class
+share/java/classes/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminantHit.class
+share/java/classes/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.class
+share/java/classes/uk/ac/babraham/FastQC/Sequence/Fast5File.class
+share/java/classes/uk/ac/babraham/FastQC/Sequence/FastQFile.class
+share/java/classes/uk/ac/babraham/FastQC/Sequence/QualityEncoding/PhredEncoding.class
+share/java/classes/uk/ac/babraham/FastQC/Sequence/Sequence.class
+share/java/classes/uk/ac/babraham/FastQC/Sequence/SequenceFactory.class
+share/java/classes/uk/ac/babraham/FastQC/Sequence/SequenceFile.class
+share/java/classes/uk/ac/babraham/FastQC/Sequence/SequenceFileGroup.class
+share/java/classes/uk/ac/babraham/FastQC/Sequence/SequenceFormatException.class
+share/java/classes/uk/ac/babraham/FastQC/Statistics/NormalDistribution.class
+share/java/classes/uk/ac/babraham/FastQC/Statistics/PearsonCorrelation.class
+share/java/classes/uk/ac/babraham/FastQC/Utilities/CasavaBasename.class
+share/java/classes/uk/ac/babraham/FastQC/Utilities/HotColdColourGradient.class
+share/java/classes/uk/ac/babraham/FastQC/Utilities/ImageToBase64.class
+share/java/classes/uk/ac/babraham/FastQC/Utilities/MultiMemberGZIPInputStream.class
+share/java/classes/uk/ac/babraham/FastQC/Utilities/NameFormatException.class
+share/java/classes/uk/ac/babraham/FastQC/Utilities/NanoporeBasename.class
+share/java/classes/uk/ac/babraham/FastQC/Utilities/QualityCount.class
+share/java/classes/uk/ac/babraham/FastQC/Utilities/RGB.class
diff --git a/fastqc/TODO b/fastqc/TODO
new file mode 100644
index 0000000000..b687356e6b
--- /dev/null
+++ b/fastqc/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/fastqc/distinfo b/fastqc/distinfo
new file mode 100644
index 0000000000..66073d1553
--- /dev/null
+++ b/fastqc/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (fastqc_v0.11.5.zip) = 4032cdb7c917c2a97952a91aa9295ab6288f93ad
+RMD160 (fastqc_v0.11.5.zip) = 2bcdbc936d9116f327909fda55cf877421fb02cf
+SHA512 (fastqc_v0.11.5.zip) = 8d12e031294fffa8601d9fbff78fbb3d7d0a7582fd0591d320f8aba856879632912080850aa06c5219dd5690b3396dee0325159ce57f59765eef4b0ce4dc9937
+Size (fastqc_v0.11.5.zip) = 10026429 bytes
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