# Migrated from BioBuilds recipe
# https://anaconda.org/BioBuilds/picard

package:
  name: picard
  version: "1.97"

source:
  fn: 1.97.tar.gz
  url: https://github.com/broadinstitute/picard/archive/1.97.tar.gz
  md5: aa5e802b7f1abcfe11e632fe52c25c08

build:
  number: 0
  skip: True # [osx]

requirements:
  build:
    - ant
    - java-jdk 6.*
    - svn

  run:
    - java-jdk 6.*

test:
  commands:
    - picard AddOrReplaceReadGroups.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard apache-ant-1.8.2-bzip2.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard BamIndexStats.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard BamToBfq.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard BuildBamIndex.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard CalculateHsMetrics.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard CheckIlluminaDirectory.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard CleanSam.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard CollectAlignmentSummaryMetrics.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard CollectGcBiasMetrics.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard CollectInsertSizeMetrics.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard CollectMultipleMetrics.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard CollectRnaSeqMetrics.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard CollectTargetedPcrMetrics.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard CompareSAMs.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard CreateSequenceDictionary.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard DownsampleSam.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard EstimateLibraryComplexity.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard ExtractIlluminaBarcodes.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard ExtractSequences.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard FastqToSam.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard FilterSamReads.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard FixMateInformation.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard IlluminaBasecallsToFastq.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard IlluminaBasecallsToSam.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard IntervalListTools.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard MakeSitesOnlyVcf.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard MarkDuplicates.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard MarkIlluminaAdapters.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard MeanQualityByCycle.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard MergeBamAlignment.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard MergeSamFiles.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard MergeVcfs.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard NormalizeFasta.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard QualityScoreDistribution.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard ReorderSam.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard ReplaceSamHeader.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard RevertSam.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard SamFormatConverter.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard SamToFastq.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard snappy-java-1.0.3-rc3.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard SortSam.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard SplitVcfs.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard tribble-1.97.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard ValidateSamFile.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard VcfFormatConverter.jar --version 2>&1 | grep '1.97' > /dev/null
    - picard ViewSam.jar --version 2>&1 | grep '1.97' > /dev/null

about:
  home: "http://broadinstitute.github.io/picard/"
  license: MIT
  summary: "Java tools for working with NGS data in the BAM format"

extra:
  notes:  "Picard version 1.97 uses a wrapper script symlinked to bin/: picard.  The wrapper script takes as arguments the particular jar file you want to run followed by any arguments for that jar.  For example, 'picard ViewSam.jar --help'."
