Re: [galaxy-dev] Get the working directory within the ncbi_blastp_wrapper.xml file

2015-10-12 Thread John Chilton
I'd keep working on pbs_python or switch to drmaa that frequently works for the same distribution. There is also a CLI runner that just executes qsub and qstat commands directly on the localhost or can also ssh into a remote host and execute these commands. https://github.com/galaxyproject/galaxy/

[galaxy-dev] Get the working directory within the ncbi_blastp_wrapper.xml file

2015-09-15 Thread Ryan Johnson
Hello all, We are setting up a galaxy instance that will submit jobs to our cluster. We could not get pbs_python to work so we have added all PBS logic to the cheetah template wrapper ncbi_blastp_wrapper.xml. Currently, all jobs are running out of the home directory. We want to add logic to