openSEQ

Forked Ubuntu 14.04 minimal install with XOrg and FluxBox desktop environment for web-based pipeline construction and job submission.

HOWTO:
1) Set VM network settings to a bridged adapter type.
2) Load VM to client
3) From host:
$ ssh -X ubuntu@<foobar> 'firefox && butterfly.server.py --unsecure'
--- passwd = 616287xx
5) or ssh into host with X forwarding, and type runme

This will launch an X-session of Firefox on the client, which will then be forwarded to the host. The first homepage tab links to our pipeline constructer. The second homepage tab links to a xterm session on the client.

Software included (location - name):
path - biobambam
path - bwa
path - bowtie2
path - bowtie
path - cufflinks
path - bcftools
path - tophat
path - scalpel
path - samtools
path - sra-toolkit
path - bamtools
path - delly
path - delly-parallel
path - picard-tools
path - fastahack
path - twoBitToFa
~/prog/java/ - mutect
~/prog/python/ - platypus
~/prog/java/ - gatk