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Attention: Research Computing Documentation has Moved

Please use the new documentation url for all Research Computing documentation needs.

As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

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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 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 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?

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.