March 2011 - galaxy-dev - lists.galaxyproject.org

getting genome coordinates
by shamsher jagat 22 Mar '11

22 Mar '11

Is it possible to extract genomic coordinates If I have gene accession ID Chr stat and end position. Any pointer will be helpful. Thanks.

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export to local file system
by James Lindsay 22 Mar '11

22 Mar '11

Hello, I was wondering if there was a way to export a dataset to the file system? Basically I think it would be advantageous if someone could copy a dataset to an "export" folder, with appropriate naming and file extensions, they could then FTP this data away or work with it locally? Thanks, James

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swap issue
by Isabelle Phan 22 Mar '11

22 Mar '11

Hello, I am running galaxy, using a postgres backend. The galaxy server systematically gets killed whenever I try uploading a bam file. The samtools process is still running. This is the end of the log: 2010-08-26 18:08:11,371 INFO sqlalchemy.engine.threadlocal.TLEngine.0x...4610 {'param_1': 8} sqlalchemy.engine.threadlocal.TLEngine.0x...4610 INFO 2010-08-26 18:08:11,371 {'param_1': 8} 2010-08-26 18:08:11,378 INFO sqlalchemy.pool.QueuePool.0x...4ed0 Connection <connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var closed: 0> being returned to pool sqlalchemy.pool.QueuePool.0x...4ed0 INFO 2010-08-26 18:08:11,378 Connection <connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var closed: 0> being returned to pool 10.1.20.44 - - [26/Aug/2010:18:08:06 -0700] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy:8080/history" "Mozilla/5.0 (X1 (x86_64); en-US; rv:1.9.2.8) Gecko/20100722 Firefox/3.6.8" Killed I have the following options set in universe_wsgi.ini: database_engine_option_server_side_cursors = True database_engine_option_strategy = threadlocal It seems to be running out of swap. I monitored memory usage with 'top' and galaxy died when available swap hit 0k free. I am not superuser on the machine where galaxy is running and I have no other server available. Is there something I could do to prevent galaxy from dying? Thanks, Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113

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Galaxy workflow with variable inputs
by Dave Walton 21 Mar '11

21 Mar '11

I'm curious if there is a way to create a workflow as follows (or if anyone else thinks this is a good idea, or for that matter has a good suggestion of another solution): 1) User selects N groomed fastq files and puts them in a history 2) User selects a workflow that allows them to select the N files, and then passes each of them to a two step process that first runs them through tophat, and the resulting bam file through cufflinks. 3) At the other end of the workflow would be a merge module that would take one of the 3 output files from cufflinks from each run, and does some sort of aggregation or transformation step on all the resulting data. Any input would be greatly appreciated. Thanks, Dave

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functional and acceptance tests
by Ryan Golhar 21 Mar '11

21 Mar '11

Are there any automated functional and/or acceptance tests that can be run on a locally installed Galaxy instance? I recently installed Galaxy here. A few people in our group have encountered problems that have taken me a bit of time to track down. Having some form of automated tests would allow me to feel confident that most of Galaxy is set up right, and track down anything I might have missed. -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

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Galaxy Local Installation Issue
by blake haas 21 Mar '11

21 Mar '11

Dear Galaxy, I had galaxy installed locally, and when I try running tophat, there is no reference genome to select, and it says "If your genome of interest is not listed, contact the Galaxy team"(below), I was wondering how I would go about solving this issue. Best, Blake Haas Select a reference genome: If your genome of interest is not listed, contact the Galaxy team

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Galaxy prone to XSS and HTML injection attacks
by Paul, Rohit (NIH/NCI) [C] 19 Mar '11

19 Mar '11

We recently ran a Nessus vulnerability scan against our server that hosts a local installation of Galaxy. The scan report showed that the web application is vulnerable to XSS and HTML injection attacks. In order to determine if/when these vulnerabilities will be fixed, where should I either send or post the scan results? -Rohit

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Re: [galaxy-dev] [galaxy-user] postgres version 9.0.3
by Dannon Baker 19 Mar '11

19 Mar '11

Martin, There were a few issues with postgres 9 that were fixed in changeset 5074, what revision is your galaxy instance running? If you are running something newer than that, could you explain more explicitly the steps to reproduce the server error? Also, I've moved the thread to galaxy-dev since this involves a local instance. -Dannon On Mar 19, 2011, at 4:45 AM, Martin Senger wrote: > Hi, > > Our system changed from postgres 8.3 to postgres 9.0.3 - and since I am getting Server error on Galaxy. I am still investigating (because the server error is not there always, specifically it does not occur for an anonymous user) but I wonder if there are some known issues with Galaxy running with postgres > 8.3. It would definitely help in my error tracking. > > Thanks, > Martin > > -- > Martin Senger > email: martin.senger@gmail.com,martin.senger@kaust.edu.sa > skype: martinsenger > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

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Workshop on Comparative Genomics, North America 2011
by Dave Clements 18 Mar '11

18 Mar '11

Hello all, Galaxy has been a part of the Workshop on Comparative Genomics held in the Czech Republic for the past several years. This two week workshop is now being offered in North America for the first time, and Galaxy will be participating again: Workshop on Comparative Genomics, North America 2011 Fort Collins, Colorado, United States July 10-22 http://www.molecularevolution.org/workshops/WCG The workshop focuses on comparative genomics using next generation sequencing data. Software packages including ABySS, Bowtie, Velvet, BioPerl, Scripture, GMOD, GBrowse_syn, PyCogent and QIME will be covered. Dan Blankenberg of the Galaxy team will teach the Galaxy sessions. There is also a Workshop on Molecular Evolution being offered immediately after the Comparative Genomics workshop. PDFs describing both events are attached. Applications for both workshops are due May 15. Thanks, Dave C -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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Metadata recursion error with empty tabular file (with patch)
by Peter Cock 18 Mar '11

18 Mar '11

Hi all, I just got a nasty recursion error when trying to run the functional tests for my TMHMM and SignalP wrappers - tools which produce tabular output. galaxy.jobs.runners.local: ERROR: Job wrapper finish method failed Traceback (most recent call last): File "/home/pjcock/repositories/galaxy-central/lib/galaxy/jobs/runners/local.py", line 125, in run_job job_wrapper.finish( stdout, stderr ) File "/home/pjcock/repositories/galaxy-central/lib/galaxy/jobs/__init__.py", line 578, in finish dataset.set_peek() File "/home/pjcock/repositories/galaxy-central/lib/galaxy/model/__init__.py", line 690, in set_peek return self.datatype.set_peek( self, is_multi_byte=is_multi_byte ) File "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/tabular.py", line 227, in set_peek data.Text.set_peek( self, dataset, line_count=line_count, is_multi_byte=is_multi_byte ) File "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/data.py", line 431, in set_peek self.set_peek(dataset) ... File "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/tabular.py", line 227, in set_peek data.Text.set_peek( self, dataset, line_count=line_count, is_multi_byte=is_multi_byte ) File "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/data.py", line 431, in set_peek self.set_peek(dataset) ... File "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/tabular.py", line 227, in set_peek data.Text.set_peek( self, dataset, line_count=line_count, is_multi_byte=is_multi_byte ) File "/home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/data.py", line 419, in set_peek dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) File "/home/pjcock/repositories/galaxy-central/lib/galaxy/model/__init__.py", line 628, in get_file_name return self.dataset.get_file_name() File "/home/pjcock/repositories/galaxy-central/lib/galaxy/model/__init__.py", line 515, in get_file_name return os.path.abspath( os.path.join( dir, "dataset_%d.dat" % self.id ) ) File "/usr/local/lib/python2.6/posixpath.py", line 348, in abspath return normpath(path) File "/usr/local/lib/python2.6/posixpath.py", line 314, in normpath slash, dot = (u'/', u'.') if isinstance(path, unicode) else ('/', '.') RuntimeError: maximum recursion depth exceeded while calling a Python object >From the trace, two set_peek methods are calling each other in a loop. I deduced the problem was an empty tabular files, where dataset.metadata.data_lines is zero, but the test should really have been for None. Please review and apply this patch which appears to correctly resolve the issue: diff -r 9fae539215be lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Fri Mar 18 11:46:48 2011 +0000 +++ b/lib/galaxy/datatypes/data.py Fri Mar 18 11:49:05 2011 +0000 @@ -422,7 +422,7 @@ dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) if line_count is None: # See if line_count is stored in the metadata - if dataset.metadata.data_lines: + if dataset.metadata.data_lines is not None: dataset.blurb = "%s %s" % ( util.commaify( str(dataset.metadata.data_lines) ), inflector.cond_plural(dataset.metadata.data_lines, "line") ) else: # Number of lines is not known ( this should not happen ), and auto-detect is Thanks, Peter

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