Hi All
We are currently using the SNP/WGS mapping strategy (described by Hobert’s Lab http://hobertlab.org/cloudmap/) to map and identify causal mutations for 20 sets of C. elegans samples. We were able to successfully use the public galaxy server and the cloudmap workflow (https://usegalaxy.org/u/gm2123/w/cloudmap-hawaiian-variant-mapping-with-wgs-and-variant-calling-workflow) for 3 sets of genome data, until we ran out of disk quota.
For the remaining samples, our best bet seems to be to setup our own local galaxy instance. The IT team in our institute had been helping us with this task, base on the guide here (http://hobertlab.org/wp-content/uploads/2013/06/GalaxySetup_and_CloudMapDependencies.pdf).
Unfortunately we are experiencing errors which we were unable to resolve when running the workflow:
Error: Unable to access jarfile /Users/pablocingolani/snpEff/snpEff.jar
Traceback (most recent call last): File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/gregory-minevich/snp_mapping_using_wgs/7fb9d1e732a0/snp_mapping_using_wgs/SNP_Mapping.py", line 10, in from rpy import * ImportError: No module named rpy
Short of trying to beat the public galaxy server’s data quota… We would appreciate any advice on either resolving these errors, accessing a “Cloudmap-ready” private server (be it collaboration, or commercial), or a dummy’s guide to getting a “cloudmap-ready” server running from scratch. Thanks in advance!