GalaxyFAQ

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=== I've set up a Personal Galaxy, now what? ===
 
=== I've set up a Personal Galaxy, now what? ===
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You could run jobs either from the command-line or from the galaxy web interface.
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# 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.
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# 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? ===

Revision as of 13:49, 11 June 2012

Contents

FAQ for Galaxy

Personal Galaxy

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.

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

You could run jobs either from the command-line or from the galaxy web interface.

  1. Command-line - Run jobs in either interactive mode or batch mode on the SGE cluster.
  2. Web interface - Follow either the DNA-Seq or 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 UAB Galaxy server from its 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?

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
sqlite> select tool_id,stdout,stderr from job where id=23;
tool_id        stdout                                stderr    
-------------  ------------------------------------  ----------
fastq_trimmer  2913558 fastq reads were processed.
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.
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