galaxy-dev December 2010

galaxy-dev@lists.galaxyproject.org

48 participants
75 discussions

Fetch closest feature
by SHAUN WEBB 12 Jan '11

12 Jan '11

Hi, I remember a post a while ago about the fetch closest feature tool requesting that the output returns overlapping features rather than just the nearest up/downstream feature. Was this ever implemented? Perhaps as a different tool? Would the easiest alternative be to create a workflow from existing tools (join-> filter out intervals that have a join -> fetch closest feature -> concatenate output files)? Thanks for your help Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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FASTA filtering by ID
by Peter 06 Jan '11

06 Jan '11

Hi all, Something I want to do in several of my workflows is to filter a FASTA file (or potentially other format sequence files) using a list of desired identifiers (e.g. a column from a tabular file). Right now I can achieve this with three steps in Galaxy. Suppose I have: Dataset #1, FASTA file Dataset #2, Tabular file with identifiers of interest (e.g. BLAST hits, or filtered output from a sequence analysis tool) Then: Create tabular Dataset #3 using FASTA-to-tabular on Dataset #1, subject to the enhancement proposed here: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003717.html Create tabular Dataset #4 using join on Datasets #2 and #3 using the matched identifier columns. This does the filtering. Create FASTA Dataset #5 using tabular-to-FASTA on Dataset #4. This works (at least for reasonably sized datasets), but requires three steps and the creation of at least two temporary files. I'd like to introduce another tool under "FASTA manipulation" to do it on one step (rather than three). Am I going against the apparent Galaxy ideal that complex manipulations should be done with tabular files? Would such a FASTA filter tool be of interest to add directly to Galaxy (e.g. under the "FASTA manipulation" section), or better off on the community tool shed? Here is my current implementation for discussion/consideration: http://bitbucket.org/peterjc/galaxy-central/changeset/730b89c4da26 Thanks, Peter

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Re: [galaxy-dev] Output files using format="input"
by Peter 06 Jan '11

06 Jan '11

On Wed, Dec 15, 2010 at 9:08 PM, James Taylor <james(a)jamestaylor.org> wrote: > > Excerpts from Peter's message of Wed Dec 15 17:18:05 +0000 2010: >> >> Is there some undocumented trick like format="input:paramname" >> where you can specify the input parameter name? > > No, but that is a great idea. > :-) In the meantime, I think I can workaround this for a short list of known formats using <change_format>, akin to the way the wrapper fastq/fastq_combiner.xml maps the FASTA and QUAL input file formats to the FASTQ output variant. Peter

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using drmaa-python
by David Hoover 03 Jan '11

03 Jan '11

Hi, I've gotten drmaa-python working for PBS Pro. Is there a resource somewhere that describes how to configure a tool for queues, node properties, etc., in the [galaxy:tool_runners] section? David Hoover Helix Systems Staff http://helix.nih.gov

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Searching in Galaxy drop down lists
by Peter 03 Jan '11

03 Jan '11

Hello all, I was finding it frustrating to use the genome select drop down in Galaxy. On the public instance there are about 800 entries (mostly bacteria), and for many organisms there are multiple entries (e.g. five releases for human). I was thinking some kind of heirachy would be useful here until I realised how well the search works. I'm now facing the same problem with other long drop down select parameters (e.g. BLAST+ databases). Can the same nice search feature be enabled in any select parameter via the tool's XML definition? Thanks, Peter

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Creating a script via a script
by Victor Ruotti 03 Jan '11

03 Jan '11

Hi, I wanted to see if there is a way to automatically create a library folder within a data library via a script. Either a bash shell or perl program. Basically a way for us to automatically add a data set based a system path and have this ready for within galaxy. Thanks in advance. Victor

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displaying data at UCSC via Galaxy using https
by Stephen Taylor 03 Jan '11

03 Jan '11

Hi, I am trying to display some data in the main public UCSC genome browser via our local Galaxy instance (based on http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications… and http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy). I removed the strip_https="True" form the bigwig.xml in display_applications/ucsc, because we only support https on our server and it seems UCSC does support retrieving data over https. When I try to view a bigWig file in Galaxy (that I have tested works via https URL directly in UCSC): "xxxx.bigwig is not a chromosome id r-tree index file" in a UCSC panel at the UCSC site. or "udc couldn't read 4 bytes from xxxx.bigwig, did read 0" (where xxxx = https URL) If I then add in my machine to the apache conf and try and see download xxxx.bigwig via a web browser I get: "Access to Galaxy is denied Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server. Please contact your local Galaxy administrator." I was assuming setting deny/allow would negate the need for a password on these files when connected to by approved servers, but perhaps I am doing something wrong here? Another question I have is should I use <Location "/display_as"> (as per http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy) or <Location "/display_application"> since their doesn't seem to be display_as in the URL. I use the same deny/allow for both to be on the safe side: <Location "/display_application"> Satisfy Any Order Deny,Allow Deny from all Allow from hgw1.cse.ucsc.edu Allow from hgw2.cse.ucsc.edu Allow from hgw3.cse.ucsc.edu Allow from hgw4.cse.ucsc.edu Allow from hgw5.cse.ucsc.edu Allow from hgw6.cse.ucsc.edu Allow from hgw7.cse.ucsc.edu Allow from hgw8.cse.ucsc.edu </Location> <Location "/display_as"> Satisfy Any Order Deny,Allow Deny from all Allow from hgw1.cse.ucsc.edu Allow from hgw2.cse.ucsc.edu Allow from hgw3.cse.ucsc.edu Allow from hgw4.cse.ucsc.edu Allow from hgw5.cse.ucsc.edu Allow from hgw6.cse.ucsc.edu Allow from hgw7.cse.ucsc.edu Allow from hgw8.cse.ucsc.edu </Location> Any ideas would be much appreciated! Thanks in advance, Steve

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blastxml to tabular bug fix
by Peter 30 Dec '10

30 Dec '10

Hi Kanwei, Could you check and commit the following three changesets from my new branch: http://bitbucket.org/peterjc/galaxy-central/src/blastplus_nov24 i.e. these three changesets: http://bitbucket.org/peterjc/galaxy-central/changeset/8f0e5a169630 http://bitbucket.org/peterjc/galaxy-central/changeset/72fab21f9469 http://bitbucket.org/peterjc/galaxy-central/changeset/72fab21f9469 This address a problem found earlier today by Alex Bossers (CC'd) while testing the BLAST+ wrappers. The problem can occur when when the query sequence is masked (with XXXX characters), this broke my calculation of the identity and mismatch counts (failing an assert statement I'd included as a sanity check). The new unit test is a cut down version of his failing example. Note that in order to run the unit tests, you will need to first re-enable the tool in tools_conf.xml.sample - the converter tests does not depend on the BLAST+ binaries being installed. Thank you, Peter

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Strange python module error
by Assaf Gordon 29 Dec '10

29 Dec '10

Hi, After upgrading to the latest galaxy-central version, I get the following exception when listing histories: =========== Error - <type 'exceptions.AttributeError'>: 'module' object has no attribute '_magic_number' File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Paste-1.6-py2.5.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/framework/middleware/remoteuser.py', line 110 in __call__ return self.app( environ, start_response ) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Paste-1.6-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/framework/__init__.py', line 84 in decorator return func( self, trans, *args, **kwargs ) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/controllers/history.py', line 235 in list return self.stored_list_grid( trans, status=status, message=message, **kwargs ) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/framework/helpers/grids.py', line 269 in __call__ kwargs=kwargs ) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/framework/__init__.py', line 645 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/data/hannon/gordon/galaxy/galaxy_prod/lib/galaxy/web/framework/__init__.py', line 656 in fill_template_mako return template.render( **data ) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 380 in _render_context (inherit, lclcontext) = _populate_self_namespace(context, tmpl) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 348 in _populate_self_namespace ret = template.module._mako_inherit(template, context) File '/data/hannon/gordon/galaxy/galaxy_prod/database/compiled_templates/history/grid.mako.py', line 24 in _mako_inherit return runtime._inherit_from(context, u'../grid_base.mako', _template_uri) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 324 in _inherit_from ret = callable_(template, lclcontext) File '/data/hannon/gordon/galaxy/galaxy_prod/database/compiled_templates/grid_base.mako.py', line 49 in _mako_inherit _mako_generate_namespaces(context) File '/data/hannon/gordon/galaxy/galaxy_prod/database/compiled_templates/grid_base.mako.py', line 45 in _mako_generate_namespaces ns = runtime.Namespace('__anon_0x19274110', context._clean_inheritance_tokens(), templateuri=u'/display_common.mako', callables=None, calling_uri=_template_uri, module=None) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 158 in __init__ self.template = _lookup_template(context, templateuri, calling_uri) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/runtime.py', line 339 in _lookup_template return lookup.get_template(uri) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/lookup.py', line 85 in get_template return self.__load(srcfile, uri) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/lookup.py', line 127 in __load self.__collection[uri] = Template(uri=uri, filename=posixpath.normpath(filename), lookup=self, module_filename=(self.modulename_callable is not None and self.modulename_callable(filename, uri) or None), **self.template_args) File '/data/hannon/gordon/galaxy/galaxy_prod/eggs/Mako-0.2.5-py2.5.egg/mako/template.py', line 85 in __init__ if module._magic_number != codegen.MAGIC_NUMBER: AttributeError: 'module' object has no attribute '_magic_number' =========== has anyone ever encountered such an error ? Any help would be appreciated. -gordon

1 1

galaxy lims issues
by Brieanne Vaillancourt 29 Dec '10

29 Dec '10

Hi, I am going to be working with Galaxy instead of Natalie Fox (at Michigan State University). I know that she was contacting you with "bugs" or "problems" that we were having with Galaxy. I have another "bug" to report and will explain below. This problem has also happened to me several times. All while in the administrator user and before the sequencing request was submitted. 1.) Select "edit" under sequencing request actions. 2.) Change name of request, request details, or anything else in the request. 3.) Save 4.) As shown in the screenshots, it says that it did save but the name and description does not change. If you could please get back to me on this as soon as possible that would be great. Thanks, Brieanne Vaillancourt /Michigan State University Research Technician/

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galaxy-dev December 2010