April 2009 - galaxy-user - lists.galaxyproject.org

An idea for sharing tools
by James Casbon 11 Jun '09

11 Jun '09

Hi Everyone, I have an "I want a pony" idea that I would like to kick onto the mailing list: It would be great if there was a way for sharing tool definitions between users. At the moment, the main repo is maintained by the galaxy team, and that is fine and makes sense. However, I'm sure there is a lot of duplicated work between the users when adding other tools in. For example, there was a conversation the other day about adding in awk. Someone had already done this, so the best idea would be if I could pull in that definition and enable it with minimum effort. I have already added tools (exonerate, restriction mapper, etc, etc) that may be of use to other people. Not sure the best way to go about this, but if my understanding of mercurial is right, we can simply offer another repo for people to pull changes from. If this is of interest to you, please can you reply? If we get enough interest and preferably some support of the core team, I could set up a free repo at, e.g., bitbucket and add users to it. Or perhaps there is a better way (eg patches submitted to trac)? Another question is what kind of tools would the core team accept for inclusion in the main dist? Cheers, James

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Exception when using remote_user.
by MORITA Hideyuki 10 Jun '09

10 Jun '09

Hi, The following error will occur under certain condition when using remote_user. AttributeError: 'NoneType' object has no attribute 'user' This error is thrown when: 1. using remote_user 2. browser has a valid session (cookie) 3. after logged in with an email address other than previously used This is caused by None value in prev_galaxy_session variable at L.231 in lib/galaxy/web/framework/__init__.py. I understand that galaxy_session instead of prev_galaxy_session should be referenced here. I created a patch to fix this problem by replacing prev_galaxy_session with galaxy_session. =================================================================================== diff -r a4214de3752e lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Tue Feb 03 18:34:27 2009 -0500 +++ b/lib/galaxy/web/framework/__init__.py Mon Feb 16 13:31:02 2009 +0900 @@ -228,7 +228,7 @@ class UniverseWebTransaction( base.Defau invalidate_existing_session = True user_for_new_session = self.__get_or_create_remote_user( remote_user_email ) log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session", - remote_user_email, prev_galaxy_session.user.email ) + remote_user_email, galaxy_session.user.email ) else: # No session exists, get/create user for new session user_for_new_session = self.__get_or_create_remote_user( remote_user_email ) =================================================================================== Thanks. MORITA Hideyuki

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unexpected formatting of parameter value of multiple check boxes
by Sebastian J. Schultheiss 01 May '09

01 May '09

Dear Galaxy team, we just discovered that a parameter in a tool description that is formatted as checkboxes gives the following output when more than one option is selected: [u'value1', u'value2'] while checking only the value1 box just yields value1 without any quotes etc. We are passing on this output to octave/matlab, where command line parameters have to be in single quotes '' in order to be recognized as strings rather than names of variables. The former output disrupts the quotation levels and was a bit unexpected. It looks it's just the __str__ representation of a python list... is that correct? Could we have an option (to preserve compatibility) to make the output look more like value1, value2 or something like that? If there already is such an option, I must have overlooked it in your ToolConfigSyntax manual and am very sorry. Thanks for your time! -- Sebastian

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Stitching MAF blocks
by Woolfe, Adam (NIH/NHGRI) [F] 30 Apr '09

30 Apr '09

Hi, On the Galaxy website there is a facility in the 'Fetch Alignments' section to 'Stitch MAF blocks given a set of genomic intervals'. I have all the Galaxy scripts also set up and would like to do the above with a command line python script but I cant find any in the python/bx-python-trunk/scripts folder that relate to stitching maf blocks together. At the moment all I can use is maf_extract_ranges_indexed.py but this doesn't stitch the blocks. Is this python script available and if so which script is it? Many thanks Adam

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password protected tool
by Roloff, Tim 24 Apr '09

24 Apr '09

Hey there, is there a "standard" way to restrict the use of certain tools by a password? Or would it even be possible to modify the list of visible tools depending on which user is logged in? Thanks Tim

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Cluster: job to User identification
by Alastair Kerr 24 Apr '09

24 Apr '09

Hi, I am looking to add galaxy to our local cluster. One of the conditions of use is that I have to ensure that any job submitted to the cluster can be traced back to an individual user. What is the easiest means to achieve this? I assume that I have to force user logins (this can be done via the universe_wsgi.ini I think). However my local install running on a single machine does not appear to list user information in the paster.log file, just the ip address. Any help much appreciated. Alastair -- Alastair Kerr, Ph.D., Bioinformatician, Wellcome Trust Centre for Cell Biology, 2.21, Michael Swann Building, Kings buildings, The University of Edinburgh, Edinburgh, EH9 3JR, UK Tel: 44-(0)131-650-7527 http://bifx1.bio.ed.ac.uk/ The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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transpose for tab-delimited file?
by Elaine Angelino 17 Apr '09

17 Apr '09

hi there! i'm very new to galaxy and it looks very cool. short version of my question: is there a way to take the transpose of a tabular file? longer: i have a tab-delimited file of SNP data, where each row corresponds to a SNP and each column corresponds to an individual (or other attribute with per-SNP information, ex. chromosome or gene information). for example, i would like to make a tab-delimited file where each row corresponds to an individual and each column corresponds to a SNP. then i would like to convert to hapmap format, etc. thanks for any help! elaine

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Error while submitting a job to sge queue
by Akash Mohan 15 Apr '09

15 Apr '09

Hi All, I have encountered this strange problem while submitting a job to an sge queue. I have used the unified method wherein the galaxy setup is made available on NFS. I have mounted the galaxy directory on the execution host. As I submit a job through the web ui I could trace that the job does get submitted to the queue. But however it fails with an error as below: galaxy.jobs.runners.sge DEBUG 2009-04-14 08:36:09,252 (15/15) state change: job finished, but failed galaxy.jobs ERROR 2009-04-14 08:36:09,493 Unable to cleanup job 15 Traceback (most recent call last): File "/usr/galaxy/galaxy-6c555b0460f1/lib/galaxy/jobs/__init__.py", line 523, in cleanup shutil.rmtree( self.working_directory ) File "/usr/local/lib/python2.5/shutil.py", line 167, in rmtree onerror(os.listdir, path, sys.exc_info()) File "/usr/local/lib/python2.5/shutil.py", line 165, in rmtree names = os.listdir(path) OSError: [Errno 2] No such file or directory: './database/job_working_directory/15' Where could error be. Kindly let me know if anybody has faced error before. Thanks a ton Akash DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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galaxy with python2.6
by Rochak Neupane 08 Apr '09

08 Apr '09

Will galaxy source be updated to be compatible with python 2.6? The README.txt file stats that it requires python 2.4 or 2.5, but I used scramble.py script to build the required eggs for 2.6. Trying to run galaxy (run.sh), I get a few warnings about deprecated modules: sets, sha. lib/galaxy/util/__init__.py:6: DeprecationWarning: the sets module is deprecated lib/galaxy/model/__init__.py:9: DeprecationWarning: the sha module is deprecated; use the hashlib module instead Once I fix that, Galaxy starts up, but I get the following error when I try to go to it from a browser. File 'build/bdist.linux-x86_64/egg/weberror/evalexception/middleware.py', line 364 in respond File 'build/bdist.linux-x86_64/egg/paste/debug/prints.py', line 98 in __call__ File 'build/bdist.linux-x86_64/egg/paste/wsgilib.py', line 539 in intercept_output File 'build/bdist.linux-x86_64/egg/beaker/session.py', line 103 in __call__ File 'build/bdist.linux-x86_64/egg/paste/recursive.py', line 80 in __call__ File 'build/bdist.linux-x86_64/egg/paste/httpexceptions.py', line 632 in __call__ File '/home/rochak/galaxy_python26/lib/galaxy/web/framework/base.py', line 124 in __call__ body = method( trans, **kwargs ) File '/home/rochak/galaxy_python26/lib/galaxy/web/controllers/root.py', line 23 in index m_c=m_c, m_a=m_a ) File '/home/rochak/galaxy_python26/lib/galaxy/web/framework/__init__.py', line 513 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/rochak/galaxy_python26/lib/galaxy/web/framework/__init__.py', line 523 in fill_template_mako return template.render( **data ) File 'build/bdist.linux-x86_64/egg/mako/template.py', line 114 in render File 'build/bdist.linux-x86_64/egg/mako/runtime.py', line 287 in _render File 'build/bdist.linux-x86_64/egg/mako/runtime.py', line 304 in _render_context File 'build/bdist.linux-x86_64/egg/mako/runtime.py', line 337 in _exec_template File '/home/rochak/galaxy_python26/database/compiled_templates/ base_panels.mako.py', line 97 in render_body context.write(unicode(next.body())) AttributeError: 'builtin_function_or_method' object has no attribute 'body' Thoughts? Thanks, Rochak

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galaxy with Python 2.6
by Rochak Neupane 08 Apr '09

08 Apr '09

Will galaxy source be updated to be compatible with python 2.6? The README.txt file stats that it requires python 2.4 or 2.5, but I used scramble.py script to build the required eggs for 2.6. Trying to run galaxy (run.sh), I get a few warnings about deprecated modules: sets, sha. lib/galaxy/util/__init__.py:6: DeprecationWarning: the sets module is deprecated lib/galaxy/model/__init__.py:9: DeprecationWarning: the sha module is deprecated; use the hashlib module instead Once I fix that, Galaxy starts up, but I get the following error when I try to go to it from a browser. File 'build/bdist.linux-x86_64/egg/weberror/evalexception/middleware.py', line 364 in respond File 'build/bdist.linux-x86_64/egg/paste/debug/prints.py', line 98 in __call__ File 'build/bdist.linux-x86_64/egg/paste/wsgilib.py', line 539 in intercept_output File 'build/bdist.linux-x86_64/egg/beaker/session.py', line 103 in __call__ File 'build/bdist.linux-x86_64/egg/paste/recursive.py', line 80 in __call__ File 'build/bdist.linux-x86_64/egg/paste/httpexceptions.py', line 632 in __call__ File '/home/rochak/galaxy_python26/lib/galaxy/web/framework/base.py', line 124 in __call__ body = method( trans, **kwargs ) File '/home/rochak/galaxy_python26/lib/galaxy/web/controllers/root.py', line 23 in index m_c=m_c, m_a=m_a ) File '/home/rochak/galaxy_python26/lib/galaxy/web/framework/__init__.py', line 513 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/rochak/galaxy_python26/lib/galaxy/web/framework/__init__.py', line 523 in fill_template_mako return template.render( **data ) File 'build/bdist.linux-x86_64/egg/mako/template.py', line 114 in render File 'build/bdist.linux-x86_64/egg/mako/runtime.py', line 287 in _render File 'build/bdist.linux-x86_64/egg/mako/runtime.py', line 304 in _render_context File 'build/bdist.linux-x86_64/egg/mako/runtime.py', line 337 in _exec_template File '/home/rochak/galaxy_python26/database/compiled_templates/ base_panels.mako.py', line 97 in render_body context.write(unicode(next.body())) AttributeError: 'builtin_function_or_method' object has no attribute 'body' Thoughts? Thanks, Rochak

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