tools.yaml

---
applications:
  ## Coming from bio_nextgen.py
  ucsc_tools: "default"
  bowtie: "0.12.9"  # Required by Tophat
  bowtie2: "2.1.0"
  # samtools: "0.1.16"  # Needs to be installed on the image
  abyss: "1.3.4"
  bfast: "0.7.0a"
  velvet: "1.2.08"
  # perm: "3.6" # Compile error
  lastz: "1.02.00"
  mosaik: "default" # Version ignored now, CBL pulls from trunk
  # macs: "1.4.1"  # From the Tool Shed

  ## Coming from bio_general.py
  # emboss:  # make error
  #   - version: "6.5.7"
  #     symlink_versions: "5.0.0"  # Setup a symbolic link, so when Galaxy looks for 5.0.0 it finds newest version

  ## Coming from applications.py
  # Tried with bio_nextgen didn't work. [ubuntu@10.1.0.3] out: No package 'gtextutils' found
  fastx_toolkit: "0.0.13.2"
  cufflinks: "2.1.1"
  tophat:
    - version: "1.3.3"
      bin_dirs: # tophat requires bowtie so make sure to include it in it's env.sh
        - bin
        - ../../bowtie/0.12.9/bin  # If bowtie from the ToolShed this will be wrong!
    - version: "2.0.9"
      bin_dirs: # tophat requires bowtie so make sure to include it in it's env.sh
        - bin
        - ../../bowtie/0.12.9/bin  # If bowtie from the ToolShed this will be wrong!
  # picard: "1.56"
  fastqc: "0.10.0"
  gatk: "1.4-9-g1f1233b"
  # maq: "0.7.1" # Compile error
  megablast: "2.2.22"
      bin_dirs: # megalblast requires blastn so make sure to include it in it's env.sh
        - .
        - ../../blast+/2.2.26+/bin
  blast:
    - version: "2.2.26+"
      requirement_name: "blast+"
  sputnik: "r1"
  taxonomy: "r2"
  add_scores: "r1"
  # hyphy: "r418" # Compile error
  srma: "0.1.15"
  beam: "2"
  pass: "2.0"
  # lps_tool: "2010.09.30"  # Anyone using this?
  plink: "1.07"
  haploview: "4.2b"
  # eigenstrat: "3.0" # Compile error
  trinity:
    - version: "r2012-10-05"
      bin_dirs:
        - .

  # bwa: "0.5.7"
  # freebayes: "2012-11-02"
  # eigenstrat: "3.0"
  # emboss: "5.0.0"
  # fbat: "2.0.3"
  # perm: "3.0"
  maq: "0.7.1"
  bedtools: "2.17.0"

r_packages:
  - DBI
  - RColorBrewer
  - RCurl
  - RSQLite
  - XML
  - biglm
  - bitops
  - digest
  - ggplot2
  - graph
  - hexbin
  - hwriter
  - kernlab
  - latticeExtra
  - leaps
  - pamr
  - plyr
  - proto
  - qvalue
  - reshape
  - statmod
  - xtable
  - yacca

bioconductor_packages:
  - AnnotationDbi
  - ArrayExpress
  - ArrayTools
  - Biobase
  - Biostrings
  - DynDoc
  - GEOquery
  - GGBase
  - GGtools
  - GSEABase
  - IRanges
  - affy
  - affyPLM
  - affyQCReport
  - affydata
  - affyio
  - annaffy
  - annotate
  - arrayQualityMetrics
  - beadarray
  - biomaRt
  - gcrma
  - genefilter
  - geneplotter
  - globaltest
  - hgu95av2.db
  - limma
  - lumi
  - makecdfenv
  - marray
  - preprocessCore
  - ShortRead
  - siggenes
  - simpleaffy
  - snpMatrix
  - vsn