GalaxyFAQ - Revision history

Ppreddy@uab.edu: /* When I hit Execute from Galaxy, does that mean the job is running on the cluster? */ Add information and steps involved in the run states of a job launched from galaxy web interface

2012-06-11T20:06:41Z

When I hit Execute from Galaxy, does that mean the job is running on the cluster?: Add information and steps involved in the run states of a job launched from galaxy web interface

← Older revision		Revision as of 20:06, 11 June 2012
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	=== When I hit ''Execute'' from Galaxy, does that mean the job is running on the cluster? ===		=== When I hit ''Execute'' from Galaxy, does that mean the job is running on the cluster? ===

			Yes. Almost all ''Execute'' operations for the tools listed in the left-hand side of the galaxy web interface result in a running a ''qsub'' job on the cluster. Once you hit the ''Execute'' button, the job goes through a series of events such as:
			# For the first few minutes after execute, you will see the watch icon next to the dataset in the History pane on the right hand side. This means that the job has been submitted to the queue and is in queue wait/hold state. Monitor this activity on the cluster by doing a ''qstat''.
			# After a while, you will see a spinning icon next to the dataset. This means the job is running on the cluster.
			# Once the spinning icon disappears, this means that the job is complete. You may perform any of the following actions to view your results:
			## View the results in the data browser (middle pane) by clicking on the ''Eye'' icon in the History pane, to the right of your dataset.
			## Click on the finished dataset itself. This displays a menu below the dataset in the History pane. The displayed options are to save, view details, run the job again, edit, annotate tags associated with the job.
			### If you click on the ''info'' icon, you can view details on the job run like, the standard output, standard error and the actual file path on the cluster where your resulting datasets are located.

	=== Where are the log files (stdout/stderr) for the job executed from Personal Galaxy? ===		=== Where are the log files (stdout/stderr) for the job executed from Personal Galaxy? ===

Ppreddy@uab.edu: /* I've set up a Personal Galaxy, now what? */ add information and links on running jobs and tutorials to follow as the next step to installing personal galaxy

2012-06-11T19:49:33Z

I've set up a Personal Galaxy, now what?: add information and links on running jobs and tutorials to follow as the next step to installing personal galaxy

← Older revision		Revision as of 19:49, 11 June 2012
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	=== I've set up a Personal Galaxy, now what? ===		=== I've set up a Personal Galaxy, now what? ===

			You could run jobs either from the command-line or from the galaxy web interface.
			# Command-line - Run jobs in either [https://dev.uabgrid.uab.edu/wiki/GalaxyUsingToolWrappersFromCommandLine#Interactivemode interactive mode] or [https://dev.uabgrid.uab.edu/wiki/GalaxyUsingToolWrappersFromCommandLine#Non-interactivemode batch mode] on the SGE cluster.
			# Web interface - Follow either the [[Galaxy_DNA-Seq_Tutorial\|DNA-Seq]] or [[UAB_Galaxy_RNA_Seq_Step_by_Step_Tutorial\|RNA-seq]] tutorials to run some NGS QC and manipulation jobs on the cluster from the galaxy web interface. The datasets related to these two tutorials can be downloaded from the [https://galaxy.uabgrid.uab.edu/ UAB Galaxy server] from its [https://galaxy.uabgrid.uab.edu/library shared data libraries.] NOTE: Access to UAB's galaxy server requires blazer-id authentication.

	=== When I hit ''Execute'' from Galaxy, does that mean the job is running on the cluster? ===		=== When I hit ''Execute'' from Galaxy, does that mean the job is running on the cluster? ===

Ppreddy@uab.edu: /* Where are the log files (stdout/stderr) for the job executed from Personal Galaxy? */ move text from new line to the list definition

2012-06-11T19:33:27Z

Where are the log files (stdout/stderr) for the job executed from Personal Galaxy?: move text from new line to the list definition

← Older revision		Revision as of 19:33, 11 June 2012
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	Galaxy provides two ways in which you can access the job's stdout and stderr content.		Galaxy provides two ways in which you can access the job's stdout and stderr content.
	:1. database		:1. database - Galaxy stores the standard out and standard error in the database. The table which contains job's stdout and stderr is ''job'' and to view the same, use the following sql query
	:Galaxy stores the standard out and standard error in the database. The table which contains job's stdout and stderr is ''job'' and to view the same, use the following sql query
	<pre>		<pre>
	sqlite> select tool_id,stdout,stderr from job where id=23;		sqlite> select tool_id,stdout,stderr from job where id=23;
Line 24:		Line 23:
	</pre>		</pre>

	:2. web interface		:2. web interface - Galaxy web interface provides an html link to the job's stdout and stderr. This can be accessed by clicking on the tool panel's (the panel on the righthand side) info button for each tool -> Tool Standard Output / Tool Standard Error links.
	:Galaxy web interface provides an html link to the job's stdout and stderr. This can be accessed by clicking on the tool panel's (the panel on the righthand side) info button for each tool -> Tool Standard Output / Tool Standard Error links.

	:During the run of the job on SGE runner, the .o (stout) and .e (stderr) files are created in the directory specified by ''$file_path'' in universe_wsgi,ini. These .o and .e files are removed automatically, once the job is complete. To preserve these two files on the file system, run galaxy in debug mode ie., set ''debug = True'' in universe_wsgi.ini.		:During the run of the job on SGE runner, the .o (stout) and .e (stderr) files are created in the directory specified by ''$file_path'' in universe_wsgi,ini. These .o and .e files are removed automatically, once the job is complete. To preserve these two files on the file system, run galaxy in debug mode ie., set ''debug = True'' in universe_wsgi.ini.

Ppreddy@uab.edu: /* Where are the log files (stdout/stderr) for the job executed from Personal Galaxy? */ explanation after personal investigations and response from psi galaxy-user uab galaxy-dev

2012-06-11T17:30:47Z

Where are the log files (stdout/stderr) for the job executed from Personal Galaxy?: explanation after personal investigations and response from psi galaxy-user uab galaxy-dev

← Older revision		Revision as of 17:30, 11 June 2012
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	=== Where are the log files (stdout/stderr) for the job executed from Personal Galaxy? ===		=== Where are the log files (stdout/stderr) for the job executed from Personal Galaxy? ===

			Galaxy provides two ways in which you can access the job's stdout and stderr content.
			:1. database
			:Galaxy stores the standard out and standard error in the database. The table which contains job's stdout and stderr is ''job'' and to view the same, use the following sql query
			<pre>
			sqlite> select tool_id,stdout,stderr from job where id=23;
			tool_id stdout stderr
			------------- ------------------------------------ ----------
			fastq_trimmer 2913558 fastq reads were processed.
			</pre>

			:2. web interface
			:Galaxy web interface provides an html link to the job's stdout and stderr. This can be accessed by clicking on the tool panel's (the panel on the righthand side) info button for each tool -> Tool Standard Output / Tool Standard Error links.

			:During the run of the job on SGE runner, the .o (stout) and .e (stderr) files are created in the directory specified by ''$file_path'' in universe_wsgi,ini. These .o and .e files are removed automatically, once the job is complete. To preserve these two files on the file system, run galaxy in debug mode ie., set ''debug = True'' in universe_wsgi.ini.

Ppreddy@uab.edu: turn sub heading to question

2012-06-08T14:40:11Z

turn sub heading to question

← Older revision		Revision as of 14:40, 8 June 2012
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	== Personal Galaxy ==		== Personal Galaxy ==

	=== ~~Error:~~ channel 3: open failed: connect failed: Connection refused ===		=== What does ''channel 3: open failed: connect failed: Connection refused'' mean? ===

	This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn \|grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number and then ssh port forward with this new port number. On Unix/Linux systems, normal users can open ports starting from 1025 to 65535.		This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn \|grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number and then ssh port forward with this new port number. On Unix/Linux systems, normal users can open ports starting from 1025 to 65535.

Jpr@uab.edu: /* Error: channel 3: open failed: connect failed: Connection refused */ Removed the emphemeral port comment. These ports are dynamically selected so shouldn't interfere.

2012-06-08T13:50:56Z

Error: channel 3: open failed: connect failed: Connection refused: Removed the emphemeral port comment. These ports are dynamically selected so shouldn't interfere.

← Older revision		Revision as of 13:50, 8 June 2012
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	=== Error: channel 3: open failed: connect failed: Connection refused ===		=== Error: channel 3: open failed: connect failed: Connection refused ===

	This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn \|grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number and then ssh port forward with this new port number. ~~Usually in~~ Unix/Linux systems, normal users can open ports starting from 1025 to 65535~~. However, some Unix/Linux systems have [http://en.wikipedia.org/wiki/Ephemeral_port Ephemeral port range] from 1025-5000. So, its safer to use a port number above 5000~~.		This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn \|grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number and then ssh port forward with this new port number. On Unix/Linux systems, normal users can open ports starting from 1025 to 65535.

	=== I've set up a Personal Galaxy, now what? ===		=== I've set up a Personal Galaxy, now what? ===

Ppreddy@uab.edu: add 3 more questions

2012-06-07T19:01:56Z

add 3 more questions

← Older revision		Revision as of 19:01, 7 June 2012
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	This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn \|grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number and then ssh port forward with this new port number. Usually in Unix/Linux systems, normal users can open ports starting from 1025 to 65535. However, some Unix/Linux systems have [http://en.wikipedia.org/wiki/Ephemeral_port Ephemeral port range] from 1025-5000. So, its safer to use a port number above 5000.		This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn \|grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number and then ssh port forward with this new port number. Usually in Unix/Linux systems, normal users can open ports starting from 1025 to 65535. However, some Unix/Linux systems have [http://en.wikipedia.org/wiki/Ephemeral_port Ephemeral port range] from 1025-5000. So, its safer to use a port number above 5000.

			=== I've set up a Personal Galaxy, now what? ===

			=== When I hit ''Execute'' from Galaxy, does that mean the job is running on the cluster? ===

			=== Where are the log files (stdout/stderr) for the job executed from Personal Galaxy? ===

Ppreddy@uab.edu: Fix sentence formation

2012-06-07T17:47:49Z

Fix sentence formation

← Older revision		Revision as of 17:47, 7 June 2012
Line 6:		Line 6:
	=== Error: channel 3: open failed: connect failed: Connection refused ===		=== Error: channel 3: open failed: connect failed: Connection refused ===

	This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn \|grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number. In Unix/Linux systems, normal users can open ports starting from 1025 to 65535. However, some Unix/Linux systems have [http://en.wikipedia.org/wiki/Ephemeral_port Ephemeral port range] from 1025-5000. So, its safer to use a port number above 5000.		This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn \|grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number and then ssh port forward with this new port number. Usually in Unix/Linux systems, normal users can open ports starting from 1025 to 65535. However, some Unix/Linux systems have [http://en.wikipedia.org/wiki/Ephemeral_port Ephemeral port range] from 1025-5000. So, its safer to use a port number above 5000.

Ppreddy@uab.edu: add TOC macro

2012-06-07T17:42:17Z

add TOC macro

← Older revision		Revision as of 17:42, 7 June 2012
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			__TOC__
	FAQ for [[Galaxy]]		FAQ for [[Galaxy]]

Ppreddy@uab.edu: /* Error: channel 3: open failed: connect failed: Connection refused */

2012-06-07T17:41:06Z

Error: channel 3: open failed: connect failed: Connection refused

← Older revision		Revision as of 17:41, 7 June 2012
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	=== Error: channel 3: open failed: connect failed: Connection refused ===		=== Error: channel 3: open failed: connect failed: Connection refused ===

	This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn \|grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number. In Unix/Linux systems, normal users can open ports starting from 1025 to 65535. However, some Unix/Linux systems have [[http://en.wikipedia.org/wiki/Ephemeral_port Ephemeral port range]] from 1025-5000. So, its safer to use a port number above 5000.		This error shows up when attempting an ssh port forwarding from the galaxy server to the localhost. This error occurs due to port conflict on the server side. The port number mentioned during the execution of ''personalize.sh'' might already be taken up ie., a service might already be running at this port. Check the list of ports opened by doing a ''netstat -lpn \|grep <port-number>''. If the result is not empty, run the ''personalize.sh'' script again with a higher port number. In Unix/Linux systems, normal users can open ports starting from 1025 to 65535. However, some Unix/Linux systems have [http://en.wikipedia.org/wiki/Ephemeral_port Ephemeral port range] from 1025-5000. So, its safer to use a port number above 5000.