Bureaucrats, cc_docs_admin, cc_staff
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Galaxy: Difference between revisions
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→Running Tools
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=== Running Tools === | === Running Tools === | ||
There are basically two ways | There are basically two ways one can run tools in a Galaxy instance. One can run them "locally", which in this case means running on the gateway machine, or one can run them by [[Running jobs|submitting jobs]] to the cluster. | ||
Please DO NOT run tools locally because the gateway machine has little memory and cannot run jobs efficiently. Galaxy | Please DO NOT run tools locally at Cedar, because the gateway machine has little memory and cannot run jobs efficiently. Galaxy is configured to submit jobs to the cluster using the file <code>job_conf.xml</code>. Some variables in this file are already set by the administrator for submitting jobs. However, you may need to optimize the entries in this file depending on the tools you will use. Please first examine the file to understand these variables and the way they are used. For example, some tools require more memory or more walltime. Please perform some tests to find out optimized job specification values for every tool you would like to run. | ||