Mercurial > repos > iuc > trinity_run_de_analysis
changeset 13:f3924bd07cba draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"
| author | iuc |
|---|---|
| date | Thu, 14 Nov 2019 04:06:09 -0500 |
| parents | fd588e138aa6 |
| children | 55cf05b65ad5 |
| files | README.rst |
| diffstat | 1 files changed, 9 insertions(+), 2 deletions(-) [+] |
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--- a/README.rst Fri Nov 01 08:11:25 2019 -0400 +++ b/README.rst Thu Nov 14 04:06:09 2019 -0500 @@ -9,7 +9,14 @@ By default, this tool is configured to limit the memory consumption to 1G. You might need to lower this limit if the machine(s) executing the jobs have less memory available. If you have a lot of reads to assemble and a machine with enough memory, you can increase it. -In both cases, you can set the GALAXY_MEMORY_MB environmental variable in the destination section of the job_conf.xml file:: + +This tool uses the GALAXY_MEMORY_MB environmental variable to limit the its memory usage. If you use a supported cluster type, you just need to limit the memory in the destination section of the job_conf.xml file to the amount of available memory (in MB), for example with a Slurm cluster:: + + <destination id="cluster_high_mem" runner="slurm + <param id="nativeSpecification">--mem=1024</param> + </destination> + +If you cluster type does not support memory limit detection, you can also set manually the GALAXY_MEMORY_MB environmental variable in the destination section of the job_conf.xml file to the amount of available memory (in MB):: <?xml version="1.0"?> <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> @@ -22,7 +29,7 @@ </handlers> <destinations> <destination id="local" runner="local"> - <env id="GALAXY_MEMORY_MB">1G</env> + <env id="GALAXY_MEMORY_MB">1024</env> </destination> </destinations> </job_conf>