Getting Cloudmap to Work on Private Galaxy Instance

Model Organism: Worms Methods & Reagents
1

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. :frowning:

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! :slight_smile:

2

Until someone more knowledgeable than me replies:

Concerning your second error, your python installation might simply be missing the rpy package.
The first error seems more tricky. Of course you need to install SnpEff, which CloudMap uses internally to annotate variants, but, in addition, the path to SnpEff seems to be hard-coded in CloudMap as /Users/pablocingolani/snpEff/snpEff.jar.
I guess you’d have to search the CloudMap Python source code to find that path and manually change it to the folder you installed SnpEff into ?

As an alternative, you may consider our own tool called MiModD (http://celegans.de/en/mimodd), which offers very similar functionality and a Galaxy interface, but is designed to be run locally and is much easier to install (see the user guide).
I’d be happy to assist you if you want to give it a try.

Best,
Wolfgang

3

For the /Users/pablocingolani/snpEff/snpEff.jar. error, we are creating that directory and putting a copy of snpEff files there, and it seems to be working ok now.

For the rpy porblem, we already have rpy installed… we are retrying using other different versions

Alright! We shall give MiModD a try if cloudmap goes nowhere :stuck_out_tongue: