Installation¶

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Requirements¶

• [cutadapt]
• [FastQC]
• samtools
• segemehl (0.2.0-420)
• haarz (comes with segemehl 0.1.7)
• metilene (v0.2-5)
• UCSC tools
• R
  • plyr
  • optparse
  • ggplot2
  • reshape2
  • gplots
  • RColorBrewer
  • grid
• perl
  • File::Basename
  • Getopt::Long
  • File::Spec
  • File::Path
  • File::Temp
  • List::Util
  • Math::Round
• Circos
• latex
• dvipdf

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Docker¶

Quick Start¶

• get docker
• pull latest docker image of BAT

docker pull christianbioinf/bat:latest

• download example dataset

wget -O - http://www.bioinf.uni-leipzig.de/Software/BAT/BAT_example_structure.tar.gz | tar -xzvf -
cd BAT_example_structure

• start docker

docker run -it --rm -w /data -v $(pwd):/data christianbioinf/bat:latest 

• run example data set and clean up from inside docker

/bin/bash run_example.sh
/bin/bash clean_example.sh