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Index: head/biology/Makefile
===================================================================
--- head/biology/Makefile
+++ head/biology/Makefile
@@ -26,6 +26,7 @@
SUBDIR += fasta3
SUBDIR += fastdnaml
SUBDIR += fastool
+ SUBDIR += fastqc
SUBDIR += fasttree
SUBDIR += fastx-toolkit
SUBDIR += fluctuate
Index: head/biology/fastqc/Makefile
===================================================================
--- head/biology/fastqc/Makefile
+++ head/biology/fastqc/Makefile
@@ -0,0 +1,43 @@
+# $FreeBSD$
+
+PORTNAME= fastqc
+DISTVERSIONPREFIX= v
+DISTVERSION= 0.11.5
+CATEGORIES= biology java perl5
+MASTER_SITES= https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+DISTNAME= ${PORTNAME}_${DISTVERSIONPREFIX}${DISTVERSION}
+
+MAINTAINER= jwb@FreeBSD.org
+COMMENT= Quality control tool for high throughput sequence data
+
+LICENSE= GPLv3
+LICENSE_FILE= ${WRKSRC}/LICENSE.txt
+
+NO_ARCH= yes
+NO_BUILD= yes
+
+USES= zip perl5 shebangfix
+SHEBANG_FILES= fastqc
+USE_JAVA= yes
+USE_PERL5= run
+
+WRKSRC= ${WRKDIR}/FastQC
+
+post-patch:
+ ${REINPLACE_CMD} \
+ -e 's|$$RealBin$$delimiter|${DATADIR}$$delimiter${JAVAJARDIR}/fastqc$$delimiter|g' \
+ -e 's|$$RealBin/|${JAVAJARDIR}/fastqc/|g' \
+ ${WRKSRC}/fastqc
+
+# Help files are not optional docs, but required for Help menu functionality
+do-install:
+ ${MKDIR} ${STAGEDIR}${JAVAJARDIR}/fastqc
+ ${INSTALL_DATA} ${WRKSRC}/*.jar ${STAGEDIR}${JAVAJARDIR}/fastqc
+ ${INSTALL_SCRIPT} ${WRKSRC}/fastqc \
+ ${STAGEDIR}${PREFIX}/bin
+ cd ${WRKSRC} && ${COPYTREE_SHARE} "Configuration Help Templates" \
+ ${STAGEDIR}${DATADIR}
+ cd ${WRKSRC} && ${COPYTREE_SHARE} "net org uk" \
+ ${STAGEDIR}${JAVAJARDIR}/fastqc
+
+.include <bsd.port.mk>
Index: head/biology/fastqc/distinfo
===================================================================
--- head/biology/fastqc/distinfo
+++ head/biology/fastqc/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1509737655
+SHA256 (fastqc_v0.11.5.zip) = dd7a5ad80ceed2588cf6d6ffe35e0f161c0d9977ed08355f5e4d9473282cbd66
+SIZE (fastqc_v0.11.5.zip) = 10026429
Index: head/biology/fastqc/pkg-descr
===================================================================
--- head/biology/fastqc/pkg-descr
+++ head/biology/fastqc/pkg-descr
@@ -0,0 +1,7 @@
+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.
+
+WWW: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Index: head/biology/fastqc/pkg-plist
===================================================================
--- head/biology/fastqc/pkg-plist
+++ head/biology/fastqc/pkg-plist
@@ -0,0 +1,206 @@
+bin/fastqc
+%%DATADIR%%/Configuration/adapter_list.txt
+%%DATADIR%%/Configuration/contaminant_list.txt
+%%DATADIR%%/Configuration/limits.txt
+%%DATADIR%%/Help/1 Introduction/1.1 What is FastQC.html
+%%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/1 Basic Statistics.html
+%%DATADIR%%/Help/3 Analysis Modules/10 Adapter Content.html
+%%DATADIR%%/Help/3 Analysis Modules/11 Kmer Content.html
+%%DATADIR%%/Help/3 Analysis Modules/12 Per Tile Sequence Quality.html
+%%DATADIR%%/Help/3 Analysis Modules/2 Per Base Sequence Quality.html
+%%DATADIR%%/Help/3 Analysis Modules/3 Per Sequence Quality Scores.html
+%%DATADIR%%/Help/3 Analysis Modules/4 Per Base Sequence Content.html
+%%DATADIR%%/Help/3 Analysis Modules/5 Per Sequence GC Content.html
+%%DATADIR%%/Help/3 Analysis Modules/6 Per Base N Content.html
+%%DATADIR%%/Help/3 Analysis Modules/7 Sequence Length Distribution.html
+%%DATADIR%%/Help/3 Analysis Modules/8 Duplicate Sequences.html
+%%DATADIR%%/Help/3 Analysis Modules/9 Overrepresented Sequences.html
+%%DATADIR%%/Help/3 Analysis Modules/duplication_levels.png
+%%DATADIR%%/Help/3 Analysis Modules/kmer_profiles.png
+%%DATADIR%%/Help/3 Analysis Modules/per_base_gc_content.png
+%%DATADIR%%/Help/3 Analysis Modules/per_base_n_content.png
+%%DATADIR%%/Help/3 Analysis Modules/per_base_quality.png
+%%DATADIR%%/Help/3 Analysis Modules/per_base_sequence_content.png
+%%DATADIR%%/Help/3 Analysis Modules/per_sequence_gc_content.png
+%%DATADIR%%/Help/3 Analysis Modules/per_sequence_quality.png
+%%DATADIR%%/Help/3 Analysis Modules/per_tile_quality.png
+%%DATADIR%%/Help/3 Analysis Modules/sequence_length_distribution.png
+%%DATADIR%%/Templates/Icons/error.png
+%%DATADIR%%/Templates/Icons/fastqc_icon.png
+%%DATADIR%%/Templates/Icons/tick.png
+%%DATADIR%%/Templates/Icons/warning.png
+%%DATADIR%%/Templates/fastqc2fo.xsl
+%%DATADIR%%/Templates/header_template.html
+%%JAVAJARDIR%%/fastqc/cisd-jhdf5.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
+%%JAVAJARDIR%%/fastqc/net/sourceforge/iharder/base64/Base64$OutputStream.class
+%%JAVAJARDIR%%/fastqc/net/sourceforge/iharder/base64/Base64.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/UnivariateFunction.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/AbstractUnivariateSolver.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/AllowedSolution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/BaseAbstractUnivariateSolver.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/BaseUnivariateSolver.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/BracketedUnivariateSolver.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/BrentSolver.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/UnivariateSolver.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/analysis/solvers/UnivariateSolverUtils.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/AbstractIntegerDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/AbstractRealDistribution$1.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/AbstractRealDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/BetaDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/BinomialDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/CauchyDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/ChiSquaredDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/FDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/GammaDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/HypergeometricDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/IntegerDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/NormalDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/PascalDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/PoissonDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/RealDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/SaddlePointExpansion.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/TDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/WeibullDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/distribution/ZipfDistribution.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/ConvergenceException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/DimensionMismatchException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/MathArithmeticException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/MathIllegalArgumentException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/MathIllegalNumberException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/MathIllegalStateException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/MathInternalError.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/MaxCountExceededException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/NoBracketingException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/NotFiniteNumberException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/NotPositiveException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/NotStrictlyPositiveException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/NullArgumentException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/NumberIsTooLargeException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/NumberIsTooSmallException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/OutOfRangeException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/TooManyEvaluationsException.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/util/ArgUtils.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/util/ExceptionContext.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/util/ExceptionContextProvider.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/util/Localizable.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/exception/util/LocalizedFormats.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/random/AbstractWell.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/random/BitsStreamGenerator.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/random/RandomData.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/random/RandomDataImpl.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/random/RandomGenerator.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/random/Well19937c.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/special/Beta$1.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/special/Beta.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/special/Erf.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/special/Gamma$1.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/special/Gamma.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/util/ArithmeticUtils.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/util/ContinuedFraction.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/util/DoubleArray.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/util/FastMath$ExpFracTable.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/util/FastMath$ExpIntTable.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/util/FastMath$lnMant.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/util/FastMath.class
+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/util/FastMathCalc.class
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+%%JAVAJARDIR%%/fastqc/org/apache/commons/math3/util/Precision.class
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