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Galaxy: Difference between revisions
→Galaxy configuration
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=== Galaxy configuration === | === Galaxy configuration === | ||
Files in the <code>config</code> directory are used to configure your Galaxy server. Configuring and optimizing Galaxy is tricky and explaining all the configuration files is beyond the scope of this article. | Files in the <code>config</code> directory are used to configure your Galaxy server. Configuring and optimizing Galaxy is tricky and explaining all the configuration files is beyond the scope of this article. If you want more information about this we recommend you read documentation on the [https://docs.galaxyproject.org/en/release_20.05/admin/config.html Galaxy website]. We list below some basic variables that are set for you by the administrator. We strongly recommend you do not change them. | ||
* In file <code>galaxy.yml</code> (the main configuration file): | * In file <code>galaxy.yml</code> (the main configuration file): | ||
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Other variables and files in this directory can be changed by the user. | |||
=== Running Tool sheds === | === Running Tool sheds === | ||
There are basically two ways to run your tool sheds, 1. run them locally which in this case means running on "gateway" machine 2. run them using job submission to cedar. Please DO NOT run tool sheds locally because gateway has small memory and it is not efficient for running jobs. Configuring Galaxy such that it submit jobs to cedar is in <code>job_conf.xml</code>. Some basic variables in this file are already set by admin for [[Running jobs|submitting jobs to Slurm]]. However, they need to be optimized for various types of tool sheds by users. Please first take a look to get families to these variables and the way they used in this files. For example some tools require more memory or more walltime. It is up to the user to optimized the corresponding variables related to each tools. | There are basically two ways to run your tool sheds, 1. run them locally which in this case means running on "gateway" machine 2. run them using job submission to cedar. Please DO NOT run tool sheds locally because gateway has small memory and it is not efficient for running jobs. Configuring Galaxy such that it submit jobs to cedar is in <code>job_conf.xml</code>. Some basic variables in this file are already set by admin for [[Running jobs|submitting jobs to Slurm]]. However, they need to be optimized for various types of tool sheds by users. Please first take a look to get families to these variables and the way they used in this files. For example some tools require more memory or more walltime. It is up to the user to optimized the corresponding variables related to each tools. | ||