external_dependencies.txt

## Tool definitions
## ================
##
## This file contains tool definitions for external tools.
##
## The record name is given by the tool. The following fields
## are available:
##
## executable: executable to test if the tool is available. Available
##             tools are in the path.
## 
## version:    options to extract the version string. If missing it is
##             assumed that a version string is displayed when the tool
##             is called without arguments
#
## regex:      regular expression to extract a version string
##
## rpackage:   the tool is an R package. The value indicates the name
##             (case-sensitive) of the R package
##           
## External tools
## ---------------
tophat:
    executable: tophat
    version: --version
    regex: '^TopHat v(\S+)'

bowtie:
    executable: bowtie
    version: --version
    regex: '^bowtie version (\S+)'

bowtie2:
    executable: bowtie2
    version: --version
    regex: 'version (\S+)'

bwa:
    executable: bwa
    regex: 'Version: (\S*)'

gsnap:
    executable: gsnap
    version: --version
    regex: 'GSNAP version (\S+) called'

star:
    executable: star
    version: --version
    regex: STAR_(\S+)

hisat:
    executable: hisat
    version: --version
    regex: 'version (\S+)'

cufflinks:
    executable: cufflinks
    regex: 'cufflinks v(\S+)'

butter:
    executable: butter
    version: --version
    regex: 'butter version (\S+)'

# part of sra-tools
fastq-dump:
    executable: fastq-dump
    version: --version
    regex: 'fastq-dump : (\S+)'

fastqc:
    executable: fastqc
    version: --version
    regex: 'FastQC v(\S+)'

fastq_screen:
    executable: fastq_screen
    version: --version
    regex: 'fastq_screen v(\S+)'

trimmomatic:
    executable: trimmomatic

cutadapt:
    executable: cutadapt
    version: --version
    regex: '(\S+)'

sickle:
    executable: sickle
    version: --version
    regex: 'sickle version (\S+)'

trimgalore:
    executable: trim_galore
    version: --version
    regex: 'version (\S+)'

flash:
    executable: flash
    version: --version
    regex: 'FLASH v(\S+)'

fastx:
    executable: fastx_trimmer
    version: -h
    regex: 'FASTX Toolkit (\S+)' 

sailfish:
    executable: sailfish
    version: --version
    regex: 'version : (\S+)'

samtools:
    executable: samtools
    regex: 'Version: (\S+)'

bedtools:
    executable: bedtools
    version: --version
    regex: 'bedtools\s+v(\S+)'

ucsctools:
    executable: bedToBigBed

picardtools:
    executable: CollectMultipleMetrics
    version: --version
    regex: '^(\S+)\('

featurecounts:
    executable: featureCounts
    version: -v
    regex: 'featureCounts v(\S+)'

bismark:
    executable: bismark
    version: --version
    regex: 'Bismark Version: v(\S+)'

stampy:
    executable: stampy.py
    regex: 'stampy v(\S+)'

macs1:
    executable: macs14
    version: --version
    regex: 'macs\S+\s+(\S+)'

macs2:
    executable: macs2
    version: --version
    regex: 'macs2\s+(\S+)'

sicer:
    executable: SICER.sh

peakranger:
    executable: peakranger
    regex: 'Version: (\S+)'

meme:
    executable: meme
    version: -version
    regex: (\S+)

# non-standard versioning (VPaperR3), so no
# version test
scripture:
    executable: scripture

broadpeak:
    executable: BroadPeak

gatk:
    executable: GenomeAnalysisTK
    version: --version
    regex: '^(\S+)-'

snpeff:
    executable: snpEff.sh
    regex: 'snpEff version SnpEff (\S+)'

gemini:
    executable: gemini

## R Packages

deseq:
    rpackage: DESeq

deseq2:
    rpackage: DESeq2

edger:
    rpackage: edgeR
    
rcolorbrewer:
    rpackage: RColorBrewer

gplots:
    rpackage: gplots

mass:
    rpackage: MASS

siggenes:
    rpackage: siggenes

ggplot2:
    rpackage: ggplot2

reshape:
    rpackage: reshape

grid:
    rpackage: grid

limma:
    rpackage: limma

samr:
    rpackage: samr

hiddenmarkov:
    rpackage: HiddenMarkov

medips:
    rpackage: MEDIPS

zinba:
    rpackage: zinba

# 11/2014: SPP seems to be not available any more
spp:
    rpackage: spp

snow:
    rpackage: snow