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Galaxy: Difference between revisions
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On cedar we provide one Galaxy instance for every research group. Galaxy installation requires a special setup that needs to be done by Compute Canada (CC) staff. If you need Galaxy for your group please write an email to support team. | On cedar we provide one Galaxy instance for every research group. Galaxy installation requires a special setup that needs to be done by Compute Canada (CC) staff. If you need Galaxy for your group please write an email to support team. | ||
=== Galaxy | === Galaxy directory structure === | ||
Galaxy is usually installed on the project directory of the group and it contains several sub-directories. The name of the Galaxy top directory is determined by taking the first two character of PI username + "glxy". For example if PI username is "davidc" the Galaxy top directory will "daglxy" and it is located in <code>/project/group name/</code> were <code>group name</code> is the default group name of PI, eg., <code>def-davidc</code>. Galaxy main directory contains the following sub-directories which is slightly different than the original Galaxy package. | Galaxy is usually installed on the project directory of the group and it contains several sub-directories. The name of the Galaxy top directory is determined by taking the first two character of PI username + "glxy". For example if PI username is "davidc" the Galaxy top directory will "daglxy" and it is located in <code>/project/group name/</code> were <code>group name</code> is the default group name of PI, eg., <code>def-davidc</code>. Galaxy main directory contains the following sub-directories which is slightly different than the original Galaxy package. | ||
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* database: It contains input, output, and error files of all jobs that run on cluster nodes. | * database: It contains input, output, and error files of all jobs that run on cluster nodes. | ||
=== Galaxy | === Galaxy files ownership and modification === | ||
All files of your Galaxy instance belong to a "pseudo-account", a shared account that is generated by an administrator at installation time. A pseudo-account does not belong to an individual person, but belongs to a specific group. Everyone in the group can log in to the pseudo-account using [https://docs.computecanada.ca/wiki/Using_SSH_keys_in_Linux SSH keys]. The name of the pseudo-account in this case is the same name as the top Galaxy directory explained above, eg., <code>daglxy</code>. In order to modify any file of your Galaxy instance, e.g. configuration files, you first need to log in to the pseudo-account. Before you can log in you must generate an SSH key pair, store your public key somewhere in your <code>home</code> directory, and let the administrator know about that. The administrator will store your public key in an appropriate place, after which you can log in to your pseudo-account. | All files of your Galaxy instance belong to a "pseudo-account", a shared account that is generated by an administrator at installation time. A pseudo-account does not belong to an individual person, but belongs to a specific group. Everyone in the group can log in to the pseudo-account using [https://docs.computecanada.ca/wiki/Using_SSH_keys_in_Linux SSH keys]. The name of the pseudo-account in this case is the same name as the top Galaxy directory explained above, eg., <code>daglxy</code>. In order to modify any file of your Galaxy instance, e.g. configuration files, you first need to log in to the pseudo-account. Before you can log in you must generate an SSH key pair, store your public key somewhere in your <code>home</code> directory, and let the administrator know about that. The administrator will store your public key in an appropriate place, after which you can log in to your pseudo-account. | ||
=== Galaxy | === Galaxy server === | ||
Do not run a Galaxy startup script on Cedar! Instead we use another machine, called a "gateway", that contains a web server with the relevant Cedar filesystems, <code>/project</code> and <code>/home</code>, mounted on it. Users cannot connect directly to the gateway due to security reasons, but you can manage your Galaxy server in this machine by going to the website [https://gateway.cedar.computecanada.ca/ https://gateway.cedar.computecanada.ca/] and following the Galaxy link. | Do not run a Galaxy startup script on Cedar! Instead we use another machine, called a "gateway", that contains a web server with the relevant Cedar filesystems, <code>/project</code> and <code>/home</code>, mounted on it. Users cannot connect directly to the gateway due to security reasons, but you can manage your Galaxy server in this machine by going to the website [https://gateway.cedar.computecanada.ca/ https://gateway.cedar.computecanada.ca/] and following the Galaxy link. | ||