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.