Bioinformatics on MonARCH
MonARCH shares the same software stack as M3, which has a number of bioinformatics packages available in the default set of modules. These include versions of:
- bwa
- bamtools
- bcftools
- bedtools
- GATK
- bcl2fastq
- BEAST
- BEAST2
- bowtie
- bowtie2
- cufflinks
- cytoscape
- fastx-toolkit
- kallisto
- macs2
- muscle
- phyml
- picard
- qiime2
- raxml
- rstudio
- samtools
- star
- sra-tools
- subread
- tophat
- varscan
- vep
- (this list shouldn't be regarded as exhaustive!)
A software stack of additional packages (known as bio-ansible) is maintained by the Monash Bioinformatics Platform (MBP).
Tools are periodically added as required by the user community.
Modules maintained by MBP are installed at: /usr/local2/bioinformatics/
To access these additional tools, type:
source /usr/local2/bioinformatics/bioansible_env.sh
This loads the bio-ansible modules into your environment alongside the default MonARCH modules. If you are using this frequently you might like to source this in your .profile / .bash_profile.
To list all modules:
module avail
You will see the additionals tools listed under the
/usr/local2/bioinformatics/software/modules/bio section, followed by
the default MonARCH modules.
Please consult the M3 Bioinformatics Community Page for full documentation on the software available.