GalaxyDocs - Revision history

Nathanrwells: /* Requesting Help */

2025-06-26T13:46:01Z

Requesting Help

← Older revision		Revision as of 08:46, 26 June 2025
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	== Requesting Help ==		== Requesting Help ==
	To request help with [https://galaxy.beocat.ksu.edu/ https://galaxy.beocat.ksu.edu/], please ~~contact <B>beocathelp@ksu.edu</B>,or~~ contact Beocat staff through a [https://support.ksu.edu/TDClient/30/Portal/Requests/ServiceDet?ID=44 TDX Ticket].<br>		To request help with [https://galaxy.beocat.ksu.edu/ https://galaxy.beocat.ksu.edu/], please contact Beocat staff through a [https://support.ksu.edu/TDClient/30/Portal/Requests/ServiceDet?ID=44 TDX Ticket].<br>
	When requesting help, it is best to give as much information as possible so that we may solve your issue in a timely manner.		When requesting help, it is best to give as much information as possible so that we may solve your issue in a timely manner.

Nathanrwells: /* Tool Requests */

2025-06-26T13:40:27Z

Tool Requests

← Older revision		Revision as of 08:40, 26 June 2025
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	== Tool Requests ==		== Tool Requests ==
	If you are missing a specific tool and would like to have it added to Galaxy, please ~~contact <B>beocathelp@ksu.edu</B> or~~ contact Beocat staff through a [https://support.ksu.edu/TDClient/30/Portal/Requests/ServiceDet?ID=44 TDX Ticket] with a link to the tool. Additionally, you can browse through Galaxy's own [https://toolshed.g2.bx.psu.edu/ toolshed] to make a recommendation.		If you are missing a specific tool and would like to have it added to Galaxy, please contact Beocat staff through a [https://support.ksu.edu/TDClient/30/Portal/Requests/ServiceDet?ID=44 TDX Ticket] with a link to the tool. Additionally, you can browse through Galaxy's own [https://toolshed.g2.bx.psu.edu/ toolshed] to make a recommendation.

	== Data Management ==		== Data Management ==

Nathanrwells at 20:12, 23 June 2025

2025-06-23T20:12:51Z

← Older revision		Revision as of 15:12, 23 June 2025
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	== Tool Requests ==		== Tool Requests ==
	If you are missing a specific tool and would like to have it added to Galaxy, please contact <B>~~beocat~~@~~cs.~~ksu.edu</B> with a link to the tool. Additionally, you can browse through Galaxy's own [https://toolshed.g2.bx.psu.edu/ toolshed] to make a recommendation.		If you are missing a specific tool and would like to have it added to Galaxy, please contact <B>beocathelp@ksu.edu</B> or contact Beocat staff through a [https://support.ksu.edu/TDClient/30/Portal/Requests/ServiceDet?ID=44 TDX Ticket] with a link to the tool. Additionally, you can browse through Galaxy's own [https://toolshed.g2.bx.psu.edu/ toolshed] to make a recommendation.

	== Data Management ==		== Data Management ==
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	== Requesting Help ==		== Requesting Help ==
	To request help with [https://galaxy.beocat.ksu.edu/ https://galaxy.beocat.ksu.edu/], please contact <B>~~beocat~~@~~cs.~~ksu.edu</B>.<br>		To request help with [https://galaxy.beocat.ksu.edu/ https://galaxy.beocat.ksu.edu/], please contact <B>beocathelp@ksu.edu</B>,or contact Beocat staff through a [https://support.ksu.edu/TDClient/30/Portal/Requests/ServiceDet?ID=44 TDX Ticket].<br>
	When requesting help, it is best to give as much information as possible so that we may solve your issue in a timely manner.		When requesting help, it is best to give as much information as possible so that we may solve your issue in a timely manner.

Nathanrwells: /* How do I access Galaxy? */

2025-04-14T17:22:21Z

How do I access Galaxy?

← Older revision		Revision as of 12:22, 14 April 2025
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	== How do I access Galaxy? ==		== How do I access Galaxy? ==
	Access to Beocat's local instance of Galaxy is easy. Simply navigate to [https://galaxy.beocat.ksu.edu/ https://galaxy.beocat.ksu.edu/] and sign in if prompted using the Keycloak login. This will use your Beocat EID and Password to login, you will also be prompted to authenticate against DUO.		Access to Beocat's local instance of Galaxy is easy. Simply navigate to [https://galaxy.beocat.ksu.edu/ https://galaxy.beocat.ksu.edu/] and sign in if prompted using the Keycloak login. This will use your Beocat EID and Password to login, you will also be prompted to authenticate against DUO.

			Please note that this utilizes Beocat's /bulk directory. This is a billed directory, and as such, if usage in your respective upload directory for Galaxy exceeds the billing threshold (1T), we will contact you regarding remediation.

	== Upload Larger Files to Galaxy ==		== Upload Larger Files to Galaxy ==

Nathanrwells at 16:31, 14 April 2025

2025-04-14T16:31:56Z

← Older revision		Revision as of 11:31, 14 April 2025
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	== How do I access Galaxy? ==		== How do I access Galaxy? ==
	Access to Beocat's local instance of Galaxy is easy. Simply navigate to [https://galaxy.beocat.ksu.edu/ https://galaxy.beocat.ksu.edu/] and sign in if prompted using the Keycloak login. This will use your Beocat EID and Password to login, you will also be prompted to authenticate against DUO.		Access to Beocat's local instance of Galaxy is easy. Simply navigate to [https://galaxy.beocat.ksu.edu/ https://galaxy.beocat.ksu.edu/] and sign in if prompted using the Keycloak login. This will use your Beocat EID and Password to login, you will also be prompted to authenticate against DUO.

			== Upload Larger Files to Galaxy ==
			Have some larger files that need to be uploaded to Galaxy? We provide some documentation on how to upload files directly to Beocat and then import them to Galaxy for use. It can be found here: [[Galaxy_File_Upload\| Galaxy File Upload]]

	== How do I use Galaxy? ==		== How do I use Galaxy? ==

Nathanrwells at 14:59, 23 August 2024

2024-08-23T14:59:46Z

← Older revision		Revision as of 09:59, 23 August 2024
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	If you fail to switch your job resource parameters, your job will submit with the default resources. This means it will submit with 5Gb of Memory and 1 CPU with 1 hour of Runtime and no Priority queue.		If you fail to switch your job resource parameters, your job will submit with the default resources. This means it will submit with 5Gb of Memory and 1 CPU with 1 hour of Runtime and no Priority queue.

	= Canceling a running job =		=== Canceling a running job ===
	While Galaxy does submit to slurm, you will not be able to cancel the job in the same way you typically do. With Galaxy, to cancel your upcoming/currently running job simply press the trash can icon next the name of your job.		While Galaxy does submit to slurm, you will not be able to cancel the job in the same way you typically do. With Galaxy, to cancel your upcoming/currently running job simply press the trash can icon next the name of your job.

Nathanrwells: /* How do I use Galaxy? */

2024-08-23T14:59:04Z

How do I use Galaxy?

← Older revision		Revision as of 09:59, 23 August 2024
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	If you fail to switch your job resource parameters, your job will submit with the default resources. This means it will submit with 5Gb of Memory and 1 CPU with 1 hour of Runtime and no Priority queue.		If you fail to switch your job resource parameters, your job will submit with the default resources. This means it will submit with 5Gb of Memory and 1 CPU with 1 hour of Runtime and no Priority queue.

			= Canceling a running job =
			While Galaxy does submit to slurm, you will not be able to cancel the job in the same way you typically do. With Galaxy, to cancel your upcoming/currently running job simply press the trash can icon next the name of your job.

	== Tool Requests ==		== Tool Requests ==

Nathanrwells: /* How do I use Galaxy? */

2024-08-20T19:00:19Z

How do I use Galaxy?

← Older revision		Revision as of 14:00, 20 August 2024
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	<B>Memory</B>: Memory size in gigabytes, 'pmem' value (1-1500). Note that the job scheduler uses --mem-per-cpu to allocate memory for your slurm job. This mean the number given for memory will be multiplied by the Processors count from above. I.e 2 Processors with 5 Memory will be 10GB of memory.<br>		<B>Memory</B>: Memory size in gigabytes, 'pmem' value (1-1500). Note that the job scheduler uses --mem-per-cpu to allocate memory for your slurm job. This mean the number given for memory will be multiplied by the Processors count from above. I.e 2 Processors with 5 Memory will be 10GB of memory.<br>
	<B>Priority Queue</B>: If you have access to a priority queue, and would like to use it, enter the partition name here.<br>		<B>Priority Queue</B>: If you have access to a priority queue, and would like to use it, enter the partition name here.<br>
	<B>Runtime</B> How long you want your job to run for in hours.		<B>Runtime</B>: How long you want your job to run for in hours.

	If you fail to switch your job resource parameters, your job will submit with the default resources. This means it will submit with 5Gb of Memory and 1 CPU with 1 hour of Runtime and no Priority queue.		If you fail to switch your job resource parameters, your job will submit with the default resources. This means it will submit with 5Gb of Memory and 1 CPU with 1 hour of Runtime and no Priority queue.

Nathanrwells: /* How do I use Galaxy? */

2024-08-20T18:58:48Z

How do I use Galaxy?

← Older revision		Revision as of 13:58, 20 August 2024
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	<B>Memory</B>: Memory size in gigabytes, 'pmem' value (1-1500). Note that the job scheduler uses --mem-per-cpu to allocate memory for your slurm job. This mean the number given for memory will be multiplied by the Processors count from above. I.e 2 Processors with 5 Memory will be 10GB of memory.<br>		<B>Memory</B>: Memory size in gigabytes, 'pmem' value (1-1500). Note that the job scheduler uses --mem-per-cpu to allocate memory for your slurm job. This mean the number given for memory will be multiplied by the Processors count from above. I.e 2 Processors with 5 Memory will be 10GB of memory.<br>
	<B>Priority Queue</B>: If you have access to a priority queue, and would like to use it, enter the partition name here.<br>		<B>Priority Queue</B>: If you have access to a priority queue, and would like to use it, enter the partition name here.<br>
	<B>Runtime</B>		<B>Runtime</B> How long you want your job to run for in hours.

	If you fail to switch your job resource parameters, your job will submit with the default resources. This means it will submit with 5Gb of Memory and 1 CPU with 1 hour of Runtime and no Priority queue.		If you fail to switch your job resource parameters, your job will submit with the default resources. This means it will submit with 5Gb of Memory and 1 CPU with 1 hour of Runtime and no Priority queue.

	== Tool Requests ==		== Tool Requests ==

Nathanrwells at 17:14, 20 August 2024

2024-08-20T17:14:16Z

← Older revision		Revision as of 12:14, 20 August 2024
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	From here you can select a tool to use and submit to the Slurm cluster. After opening a tool you will be given options (if available) to configure the tool, including its inputs, what the tool will do (within its constraints) outputs, and what compute resources the tool will submit with. This means that you can specify the resources given to slurm jobs by expanding the drop-down menu "Job Resource Paramters" and selecting "Specify Job resource parameters" which will show the following options to modify.		From here you can select a tool to use and submit to the Slurm cluster. After opening a tool you will be given options (if available) to configure the tool, including its inputs, what the tool will do (within its constraints) outputs, and what compute resources the tool will submit with. This means that you can specify the resources given to slurm jobs by expanding the drop-down menu "Job Resource Paramters" and selecting "Specify Job resource parameters" which will show the following options to modify.

	<B>Processors</B>Number of processing cores, 'ppn' value (1-128) this is equivalent to slurms "--cpus-per-task".<br>		<B>Processors</B>: Number of processing cores, 'ppn' value (1-128) this is equivalent to slurms "--cpus-per-task".<br>
	<B>Memory</B>Memory size in gigabytes, 'pmem' value (1-1500). Note that the job scheduler uses --mem-per-cpu to allocate memory for your slurm job. This mean the number given for memory will be multiplied by the Processors count from above. I.e 2 Processors with 5 Memory will be 10GB of memory.<br>		<B>Memory</B>: Memory size in gigabytes, 'pmem' value (1-1500). Note that the job scheduler uses --mem-per-cpu to allocate memory for your slurm job. This mean the number given for memory will be multiplied by the Processors count from above. I.e 2 Processors with 5 Memory will be 10GB of memory.<br>
	<B>Priority Queue</B>If you have access to a priority queue, and would like to use it, enter the partition name here.<br>		<B>Priority Queue</B>: If you have access to a priority queue, and would like to use it, enter the partition name here.<br>
	<B>Runtime</B>		<B>Runtime</B>