Hi all, I am trying to set up my own galaxy server (and I don't know much IT) and thought that I had my sge working properly, but when I try to load data -- via manage data libraries on the web interface, I get the following error:
/bin/sh: module: line 1: syntax error: unexpected end of file /bin/sh: error importing function definition for `module'
This works if I do not use SGE.
Anyone know what this error could mean??
Here are the 2 lines in universal_wsgi.ini that are used for SGE:
default_cluster_job_runner = drmaa://-V -v TMPDIR=/scratch/ job_config_file = job_conf.xml
Here is my job_conf.xml file:
<?xml version="1.0"?> <job_conf> <plugins workers="4"> <!-- "workers" is the number of threads for the runner's work queue. The default from <plugins> is used if not defined for a <plugin>. --> <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/> </plugins> <handlers default="handlers"> <!-- Additional job handlers - the id should match the name of a [server:<id>] in universe_wsgi.ini. --> <handler id="main" tags="handlers"/> </handlers> <destinations default="sge_default"> <!-- Destinations define details about remote resources and how jobs should be executed on those remote resources. --> <destination id="sge_default" runner="sge"> <param id="nativeSpecification">-V</param> </destination> <!-- Define parameters that are native to the job runner plugin. --> </destinations> </job_conf>
Thanks! ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Brandi Cantarel, PhD Bioinformatics Research Scientist Baylor Institute for Immunology Research Baylor Health Care System 214-820-9064 (office)
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