Error while using MutSigCV on the new cloud server

[Théo Hirsch]

Hello,

I tried to run MutSigCV from the new cloud server. As inputs, I used:

- my own mutation table (in the same format as what used to work on the broad server)

- coverage table: ftp://gpftp.broadinstitute.org/module_support_files/MutSigCV_1.4/exome_full192.coverage.txt

- covariate table: ftp://gpftp.broadinstitute.org/module_support_files/MutSigCV_1.4/gene.covariates.txt

- mutation type dictionary: ftp://gpftp.broadinstitute.org/module_support_files/MutSigCV_1.4/mutation_type_dictionary_file.txt

I got an error with the following message in stderr.txt:

/opt/gpbeta/gp_home/resources/wrapper_scripts/gp-common.sh: line 598: /opt/gpbeta/gp_home/taskLib/MutSigCV.1.2.217/gp_MutSigCV: Permission denied

Do you know what it means? For information, I then tried to run it with the same mutation table on the broad server (but with the 1.3 versions of the input parameters) and it did work.

Thank you in advance !

[Barbara Hill]

Hello, 

Thank you for bringing this to our attention. This module needs to be updated to run in Docker on our new cloud server.

We will add this to our work in the next few weeks and let you know when we have a new functional version available.

Best

-Barbara