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Galaxy: Difference between revisions
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→Running Tool sheds
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Other variables and files in this directory can be changed by the user. | Other variables and files in this directory can be changed by the user. | ||
=== Running | === Running Tools === | ||
There are basically two ways to run your | There are basically two ways to run your tools in your Galaxy instance. You can run them locally, which in this case means running on the gateway machine, or you can run them using job submission to cedar cluster. | ||
Please DO NOT run tool sheds locally because the gateway machine has little memory and cannot run jobs efficiently. Galaxy can be 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 [[Running jobs|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 DO NOT run tool sheds locally because the gateway machine has little memory and cannot run jobs efficiently. Galaxy can be 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 [[Running jobs|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 tools you would like to run. | ||