Galaxy: Difference between revisions

Galaxy (view source)

Revision as of 09:32, 14 January 2021

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→‎Galaxy configuration

Aroudgar

cc_staff

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 === 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. For more information we recommend you to take a look at galaxy website documentation.   We have set some of these variable for you so that your Galaxy server works in our HPC environment. Here we explain some of these variables and we strongly recommend not to change them.
+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. For more information we recommend you to take a look at galaxy website documentation.  In this section we explained some basic variables that has been set by admin and we strongly recommend not to change them. Below is the list of these variables:
-* File <code>galaxy.yml</code>: its most important and the main configuration file. The following variables are set in this file:
+* In file <code>galaxy.yml</code> (the main configuration file):
 ** <code>http:</code> contains your unique port number
 ** <code>database_connection</code> is the name of your Galaxy database and your database server.
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 ** <code>file_path, new_file_path, tool_config_file, shed_tool_config_file, tool_dependency_dir, tool_data_path, visualization_plugins_directory, job_working_directory, cluster_files_directory, template_cache_path, citation_cache_data_dir, citation_cache_lock_dir</code> are appropriate paths for tools, tool sheds and dependencies.
-* <code>job_conf.xml</code>: Variables in this file are used for [[Running jobs|submitting jobs to Slurm]]. Various packages have different job specifications. For example, package "spades" uses 8 cores with a wall-time of 3 hours and the job will be submitted under your default group name <code>def-xxxxx</code>. Please take a look at this file and set up your desired job specifications. Note that any change in these configuration files requires the server to be restarted.
+The rest of variables  and files in this directory can be changed by user.
+==== 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.