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test-nginx01 & pg02
Port details
fastqc Quality control tool for high throughput sequence data
0.11.5 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 30 Nov 2017 22:54:38
Also Listed In: java perl5
License: GPLv3
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/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (209 items)
  1. /usr/local/share/licenses/fastqc-0.11.5/catalog.mk
  2. /usr/local/share/licenses/fastqc-0.11.5/LICENSE
  3. /usr/local/share/licenses/fastqc-0.11.5/GPLv3
  4. bin/fastqc
  5. share/fastqc/Configuration/adapter_list.txt
  6. share/fastqc/Configuration/contaminant_list.txt
  7. share/fastqc/Configuration/limits.txt
  8. share/fastqc/Help/1 Introduction/1.1 What is FastQC.html
  9. share/fastqc/Help/2 Basic Operations/2.1 Opening a sequence file.html
  10. share/fastqc/Help/2 Basic Operations/2.2 Evaluating Results.html
  11. share/fastqc/Help/2 Basic Operations/2.3 Saving a Report.html
  12. share/fastqc/Help/3 Analysis Modules/1 Basic Statistics.html
  13. share/fastqc/Help/3 Analysis Modules/10 Adapter Content.html
  14. share/fastqc/Help/3 Analysis Modules/11 Kmer Content.html
  15. share/fastqc/Help/3 Analysis Modules/12 Per Tile Sequence Quality.html
  16. share/fastqc/Help/3 Analysis Modules/2 Per Base Sequence Quality.html
  17. share/fastqc/Help/3 Analysis Modules/3 Per Sequence Quality Scores.html
  18. share/fastqc/Help/3 Analysis Modules/4 Per Base Sequence Content.html
  19. share/fastqc/Help/3 Analysis Modules/5 Per Sequence GC Content.html
  20. share/fastqc/Help/3 Analysis Modules/6 Per Base N Content.html
  21. share/fastqc/Help/3 Analysis Modules/7 Sequence Length Distribution.html
  22. share/fastqc/Help/3 Analysis Modules/8 Duplicate Sequences.html
  23. share/fastqc/Help/3 Analysis Modules/9 Overrepresented Sequences.html
  24. share/fastqc/Help/3 Analysis Modules/duplication_levels.png
  25. share/fastqc/Help/3 Analysis Modules/kmer_profiles.png
  26. share/fastqc/Help/3 Analysis Modules/per_base_gc_content.png
  27. share/fastqc/Help/3 Analysis Modules/per_base_n_content.png
  28. share/fastqc/Help/3 Analysis Modules/per_base_quality.png
  29. share/fastqc/Help/3 Analysis Modules/per_base_sequence_content.png
  30. share/fastqc/Help/3 Analysis Modules/per_sequence_gc_content.png
  31. share/fastqc/Help/3 Analysis Modules/per_sequence_quality.png
  32. share/fastqc/Help/3 Analysis Modules/per_tile_quality.png
  33. share/fastqc/Help/3 Analysis Modules/sequence_length_distribution.png
  34. share/fastqc/Templates/Icons/error.png
  35. share/fastqc/Templates/Icons/fastqc_icon.png
  36. share/fastqc/Templates/Icons/tick.png
  37. share/fastqc/Templates/Icons/warning.png
  38. share/fastqc/Templates/fastqc2fo.xsl
  39. share/fastqc/Templates/header_template.html
  40. share/java/classes/fastqc/cisd-jhdf5.jar
  41. share/java/classes/fastqc/jbzip2-0.9.jar
  42. share/java/classes/fastqc/net/sourceforge/iharder/base64/Base64$1.class
  43. share/java/classes/fastqc/net/sourceforge/iharder/base64/Base64$InputStream.class
  44. share/java/classes/fastqc/net/sourceforge/iharder/base64/Base64$OutputStream.class
  45. share/java/classes/fastqc/net/sourceforge/iharder/base64/Base64.class
  46. share/java/classes/fastqc/org/apache/commons/math3/analysis/UnivariateFunction.class
  47. share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/AbstractUnivariateSolver.class
  48. share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/AllowedSolution.class
  49. share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/BaseAbstractUnivariateSolver.class
  50. share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/BaseUnivariateSolver.class
  51. share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/BracketedUnivariateSolver.class
  52. share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/BrentSolver.class
  53. share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/UnivariateSolver.class
  54. share/java/classes/fastqc/org/apache/commons/math3/analysis/solvers/UnivariateSolverUtils.class
  55. share/java/classes/fastqc/org/apache/commons/math3/distribution/AbstractIntegerDistribution.class
  56. share/java/classes/fastqc/org/apache/commons/math3/distribution/AbstractRealDistribution$1.class
  57. share/java/classes/fastqc/org/apache/commons/math3/distribution/AbstractRealDistribution.class
  58. share/java/classes/fastqc/org/apache/commons/math3/distribution/BetaDistribution.class
  59. share/java/classes/fastqc/org/apache/commons/math3/distribution/BinomialDistribution.class
  60. share/java/classes/fastqc/org/apache/commons/math3/distribution/CauchyDistribution.class
  61. share/java/classes/fastqc/org/apache/commons/math3/distribution/ChiSquaredDistribution.class
  62. share/java/classes/fastqc/org/apache/commons/math3/distribution/FDistribution.class
  63. share/java/classes/fastqc/org/apache/commons/math3/distribution/GammaDistribution.class
  64. share/java/classes/fastqc/org/apache/commons/math3/distribution/HypergeometricDistribution.class
  65. share/java/classes/fastqc/org/apache/commons/math3/distribution/IntegerDistribution.class
  66. share/java/classes/fastqc/org/apache/commons/math3/distribution/NormalDistribution.class
  67. share/java/classes/fastqc/org/apache/commons/math3/distribution/PascalDistribution.class
  68. share/java/classes/fastqc/org/apache/commons/math3/distribution/PoissonDistribution.class
  69. share/java/classes/fastqc/org/apache/commons/math3/distribution/RealDistribution.class
  70. share/java/classes/fastqc/org/apache/commons/math3/distribution/SaddlePointExpansion.class
  71. share/java/classes/fastqc/org/apache/commons/math3/distribution/TDistribution.class
  72. share/java/classes/fastqc/org/apache/commons/math3/distribution/WeibullDistribution.class
  73. share/java/classes/fastqc/org/apache/commons/math3/distribution/ZipfDistribution.class
  74. share/java/classes/fastqc/org/apache/commons/math3/exception/ConvergenceException.class
  75. share/java/classes/fastqc/org/apache/commons/math3/exception/DimensionMismatchException.class
  76. share/java/classes/fastqc/org/apache/commons/math3/exception/MathArithmeticException.class
  77. share/java/classes/fastqc/org/apache/commons/math3/exception/MathIllegalArgumentException.class
  78. share/java/classes/fastqc/org/apache/commons/math3/exception/MathIllegalNumberException.class
  79. share/java/classes/fastqc/org/apache/commons/math3/exception/MathIllegalStateException.class
  80. share/java/classes/fastqc/org/apache/commons/math3/exception/MathInternalError.class
  81. share/java/classes/fastqc/org/apache/commons/math3/exception/MaxCountExceededException.class
  82. share/java/classes/fastqc/org/apache/commons/math3/exception/NoBracketingException.class
  83. share/java/classes/fastqc/org/apache/commons/math3/exception/NotFiniteNumberException.class
  84. share/java/classes/fastqc/org/apache/commons/math3/exception/NotPositiveException.class
  85. share/java/classes/fastqc/org/apache/commons/math3/exception/NotStrictlyPositiveException.class
  86. share/java/classes/fastqc/org/apache/commons/math3/exception/NullArgumentException.class
  87. share/java/classes/fastqc/org/apache/commons/math3/exception/NumberIsTooLargeException.class
  88. share/java/classes/fastqc/org/apache/commons/math3/exception/NumberIsTooSmallException.class
  89. share/java/classes/fastqc/org/apache/commons/math3/exception/OutOfRangeException.class
  90. share/java/classes/fastqc/org/apache/commons/math3/exception/TooManyEvaluationsException.class
  91. share/java/classes/fastqc/org/apache/commons/math3/exception/util/ArgUtils.class
  92. share/java/classes/fastqc/org/apache/commons/math3/exception/util/ExceptionContext.class
  93. share/java/classes/fastqc/org/apache/commons/math3/exception/util/ExceptionContextProvider.class
  94. share/java/classes/fastqc/org/apache/commons/math3/exception/util/Localizable.class
  95. share/java/classes/fastqc/org/apache/commons/math3/exception/util/LocalizedFormats.class
  96. share/java/classes/fastqc/org/apache/commons/math3/random/AbstractWell.class
  97. share/java/classes/fastqc/org/apache/commons/math3/random/BitsStreamGenerator.class
  98. share/java/classes/fastqc/org/apache/commons/math3/random/RandomData.class
  99. share/java/classes/fastqc/org/apache/commons/math3/random/RandomDataImpl.class
  100. share/java/classes/fastqc/org/apache/commons/math3/random/RandomGenerator.class
  101. share/java/classes/fastqc/org/apache/commons/math3/random/Well19937c.class
  102. share/java/classes/fastqc/org/apache/commons/math3/special/Beta$1.class
  103. share/java/classes/fastqc/org/apache/commons/math3/special/Beta.class
  104. share/java/classes/fastqc/org/apache/commons/math3/special/Erf.class
  105. share/java/classes/fastqc/org/apache/commons/math3/special/Gamma$1.class
  106. share/java/classes/fastqc/org/apache/commons/math3/special/Gamma.class
  107. share/java/classes/fastqc/org/apache/commons/math3/util/ArithmeticUtils.class
  108. share/java/classes/fastqc/org/apache/commons/math3/util/ContinuedFraction.class
  109. share/java/classes/fastqc/org/apache/commons/math3/util/DoubleArray.class
  110. share/java/classes/fastqc/org/apache/commons/math3/util/FastMath$ExpFracTable.class
  111. share/java/classes/fastqc/org/apache/commons/math3/util/FastMath$ExpIntTable.class
  112. share/java/classes/fastqc/org/apache/commons/math3/util/FastMath$lnMant.class
  113. share/java/classes/fastqc/org/apache/commons/math3/util/FastMath.class
  114. share/java/classes/fastqc/org/apache/commons/math3/util/FastMathCalc.class
  115. share/java/classes/fastqc/org/apache/commons/math3/util/FastMathLiteralArrays.class
  116. share/java/classes/fastqc/org/apache/commons/math3/util/Incrementor$1.class
  117. share/java/classes/fastqc/org/apache/commons/math3/util/Incrementor$MaxCountExceededCallback.class
  118. share/java/classes/fastqc/org/apache/commons/math3/util/Incrementor.class
  119. share/java/classes/fastqc/org/apache/commons/math3/util/MathUtils.class
  120. share/java/classes/fastqc/org/apache/commons/math3/util/Precision.class
  121. share/java/classes/fastqc/org/apache/commons/math3/util/ResizableDoubleArray.class
  122. share/java/classes/fastqc/sam-1.103.jar
  123. share/java/classes/fastqc/uk/ac/babraham/FastQC/Analysis/AnalysisListener.class
  124. share/java/classes/fastqc/uk/ac/babraham/FastQC/Analysis/AnalysisQueue.class
  125. share/java/classes/fastqc/uk/ac/babraham/FastQC/Analysis/AnalysisRunner.class
  126. share/java/classes/fastqc/uk/ac/babraham/FastQC/Analysis/OfflineRunner.class
  127. share/java/classes/fastqc/uk/ac/babraham/FastQC/Dialogs/AboutDialog$1.class
  128. share/java/classes/fastqc/uk/ac/babraham/FastQC/Dialogs/AboutDialog.class
  129. share/java/classes/fastqc/uk/ac/babraham/FastQC/Dialogs/FastQCTitlePanel$SmoothJLabel.class
  130. share/java/classes/fastqc/uk/ac/babraham/FastQC/Dialogs/FastQCTitlePanel.class
  131. share/java/classes/fastqc/uk/ac/babraham/FastQC/Dialogs/WelcomePanel.class
  132. share/java/classes/fastqc/uk/ac/babraham/FastQC/FastQCApplication$1.class
  133. share/java/classes/fastqc/uk/ac/babraham/FastQC/FastQCApplication.class
  134. share/java/classes/fastqc/uk/ac/babraham/FastQC/FastQCConfig.class
  135. share/java/classes/fastqc/uk/ac/babraham/FastQC/FastQCMenuBar.class
  136. share/java/classes/fastqc/uk/ac/babraham/FastQC/FileFilters/BAMFileFilter.class
  137. share/java/classes/fastqc/uk/ac/babraham/FastQC/FileFilters/CasavaFastQFileFilter.class
  138. share/java/classes/fastqc/uk/ac/babraham/FastQC/FileFilters/FastQFileFilter.class
  139. share/java/classes/fastqc/uk/ac/babraham/FastQC/FileFilters/GobyFileFilter.class
  140. share/java/classes/fastqc/uk/ac/babraham/FastQC/FileFilters/MappedBAMFileFilter.class
  141. share/java/classes/fastqc/uk/ac/babraham/FastQC/FileFilters/SequenceFileFilter.class
  142. share/java/classes/fastqc/uk/ac/babraham/FastQC/Graphs/BaseGroup.class
  143. share/java/classes/fastqc/uk/ac/babraham/FastQC/Graphs/LineGraph.class
  144. share/java/classes/fastqc/uk/ac/babraham/FastQC/Graphs/QualityBoxPlot.class
  145. share/java/classes/fastqc/uk/ac/babraham/FastQC/Graphs/TileGraph.class
  146. share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpDialog.class
  147. share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpIndexRoot$FileSorter.class
  148. share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpIndexRoot.class
  149. share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpPage.class
  150. share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpPageDisplay$HelpEditor.class
  151. share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpPageDisplay.class
  152. share/java/classes/fastqc/uk/ac/babraham/FastQC/Help/HelpSearchPanel.class
  153. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/AbstractQCModule.class
  154. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/AdapterContent$Adapter.class
  155. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/AdapterContent$ResultsTable.class
  156. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/AdapterContent.class
  157. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/BasicStats$ResultsTable.class
  158. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/BasicStats.class
  159. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/DuplicationLevel.class
  160. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/GCModel/GCModel.class
  161. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/GCModel/GCModelValue.class
  162. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/KmerContent$Kmer.class
  163. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/KmerContent$ResultsTable.class
  164. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/KmerContent.class
  165. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/ModuleConfig.class
  166. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/ModuleFactory.class
  167. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/NContent.class
  168. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs$OverrepresentedSeq.class
  169. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs$ResultsTable.class
  170. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/OverRepresentedSeqs.class
  171. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/PerBaseQualityScores.class
  172. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/PerBaseSequenceContent.class
  173. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/PerSequenceGCContent.class
  174. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/PerSequenceQualityScores.class
  175. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/PerTileQualityScores.class
  176. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/QCModule.class
  177. share/java/classes/fastqc/uk/ac/babraham/FastQC/Modules/SequenceLengthDistribution.class
  178. share/java/classes/fastqc/uk/ac/babraham/FastQC/Report/HTMLReportArchive.class
  179. share/java/classes/fastqc/uk/ac/babraham/FastQC/Report/stylesheet.txt
  180. share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/error.png
  181. share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/fastqc_icon.png
  182. share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/fastqc_icon.svg
  183. share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/fastqc_icon_100.png
  184. share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/tick.png
  185. share/java/classes/fastqc/uk/ac/babraham/FastQC/Resources/warning.png
  186. share/java/classes/fastqc/uk/ac/babraham/FastQC/Results/ResultsPanel$ModuleRenderer.class
  187. share/java/classes/fastqc/uk/ac/babraham/FastQC/Results/ResultsPanel.class
  188. share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/BAMFile.class
  189. share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Contaminant/Contaminant.class
  190. share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminantHit.class
  191. share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.class
  192. share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.class
  193. share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/FastQFile.class
  194. share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/QualityEncoding/PhredEncoding.class
  195. share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/Sequence.class
  196. share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFactory.class
  197. share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFile.class
  198. share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFileGroup.class
  199. share/java/classes/fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFormatException.class
  200. share/java/classes/fastqc/uk/ac/babraham/FastQC/Statistics/NormalDistribution.class
  201. share/java/classes/fastqc/uk/ac/babraham/FastQC/Statistics/PearsonCorrelation.class
  202. share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/CasavaBasename.class
  203. share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/HotColdColourGradient.class
  204. share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/ImageToBase64.class
  205. share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/MultiMemberGZIPInputStream.class
  206. share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/NameFormatException.class
  207. share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/NanoporeBasename.class
  208. share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/QualityCount.class
  209. share/java/classes/fastqc/uk/ac/babraham/FastQC/Utilities/RGB.class
  210. Collapse this list.

To install the port: cd /usr/ports/biology/fastqc/ && make install clean
To add the package: pkg install fastqc

PKGNAME: fastqc

distinfo:

TIMESTAMP = 1509737655
SHA256 (fastqc_v0.11.5.zip) = dd7a5ad80ceed2588cf6d6ffe35e0f161c0d9977ed08355f5e4d9473282cbd66
SIZE (fastqc_v0.11.5.zip) = 10026429


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Runtime dependencies:
  1. java : java/openjdk8
  2. perl5>=5.24<5.25 : lang/perl5.24

This port is required by:

for Run * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...
Configuration Options
     No options to configure

USES:
zip perl5 shebangfix

Master Sites:
  1. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Number of commits found: 1

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
30 Nov 2017 22:54:29
Original commit files touched by this commit  0.11.5
Revision:455236
jwb search for other commits by this committer
[new port] biology/fastqc: Quality control tool for high throughput sequence
data

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13304

Number of commits found: 1

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