- galaxy-dev - lists.galaxyproject.org

15 Apr '11

ERROR:" Can't access SIFT output file "/home/galaxy/galaxy-python/galaxy-dist/database/job_working_directory/537/20452/20452_predictions.tsv" " Hi, I'm using a local instance and I'm getting this error when running the SIFT tool. The database is installed... but it seems that is unable to generate the .tsv final file. I would appreciate any advise regarding this issue, Thanks in advance. Ben.

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java client integration????
by Reema Popley 15 Apr '11

15 Apr '11

Hi i have java client of my tools i need to integrate them in galaxy..so i basically need to convert dose java client into xml.....but i m not sure whether java clients can be integrated in galaxy or not...please let me knw d same....Thank you

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uploading a large number of files to a library
by Glen Beane 15 Apr '11

15 Apr '11

I have been having trouble uploading a large number of fastq files to a library (180). I am uploading a directory of files, and I am not copying the files into Galaxy. When I try to view the files in the library after uploading it takes a long time to load the library view (sometimes it times out), and when it does load it lists every file three times so instead of there being 180 fastq files in the library there are 540. I have tried this multiple times after deleting the library and starting over, and each time it looks like there are three copies of each file. Has anyone else had trouble uploading a large number of fastq files into a library at the same time? I tried to delete a bunch of the duplicate files but it just timed out. -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153

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Error in user registration
by Sarah Diehl 15 Apr '11

15 Apr '11

Hello, it seems since I updated to the newest galaxy-dist, I always get an error when trying to register a new user. When I try it from the admin panel, the error is the following: Error - <type 'exceptions.NameError'>: Undefined URL: http://solweb2.immunbio.mpg.de/user/create?cntrller=admin&webapp=galaxy File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/user.py', line 523 in create status=status ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 650 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako return template.render( **data ) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in <lambda> return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 69 in render_body __M_writer(unicode(render_registration_form())) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 40 in render_registration_form return render_render_registration_form(context.locals_(__M_locals),form_action) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 121 in render_render_registration_form form_action = h.url_for( controller='user', action='create', admin_view=admin_view ) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/util.py', line 248 in url_for url = config.mapper.generate(*route_args, **newargs) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/mapper.py', line 823 in generate path = route.generate(**kargs) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/route.py', line 736 in generate fragments.append((key, _str_encode(val, self.encoding))) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/util.py', line 129 in _str_encode s = unicode(string).encode(encoding) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 128 in __str__ raise NameError("Undefined") NameError: Undefined If I log out and try it from the "User" menu, I get the following error: Error - <type 'exceptions.TypeError'>: create() takes at least 3 arguments (2 given) URL: http://solweb2.immunbio.mpg.de/user/create File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) TypeError: create() takes at least 3 arguments (2 given) I have no idea what is going on, any help is greatly appreciated, thank you! Best regards, Sarah Diehl

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script to download genomes
by James Lindsay 14 Apr '11

14 Apr '11

Hello, I'm working on a simple python script that auto-magically creates all indexes, and pre-processing necessary to add a genome to galaxy. I was wondering if anyone had a script to download all the genomes that are presented to you in the default genome drop down box? Also I'm not to confident about what "all" preprocessing actually is (with respect to the default configuration). So far I create the create indexes for the following tools and add their appropriate entry into their tools-data config file: sam index bowtie, base/color bwa, base/color bfast, base (any advice on how to do color?) blast (n and p) Am I missing any tool that requires preprocessing? Thanks, James

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Re: [galaxy-dev] Trouble setting up Galaxy with apache proxy
by Paul-Michael Agapow 14 Apr '11

14 Apr '11

> I used this step by step : > > https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy > > to set up galaxy with apache proxy. > > I face a problem with the history panel which always displays : "Your > history is empty. Click 'Get Data' on the left pane to start >. Even if I > upload Data, even if I log into galaxy. Bernard, I had the same problem with a Galaxy instance proxied through Apache, with the other proximate symptom being that I was never actually logged into Galaxy, and thus never saw any history. (Logging in would seemingly have no effect.) Eventually I traced it to a problem with cookies: galaxy instances distinguish users by the cookie_path setting in the config file and I posit that me using that instance of Galaxy through and not through the proxy had caused some confusion. Solution: delete cookies. I could then log in properly. ---- Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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Trouble setting up Galaxy with apache proxy
by Bertrand Pitollat 14 Apr '11

14 Apr '11

I used this step by step : https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy to set up galaxy with apache proxy. I added these lines to httpd.conf file : RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /usr/local/bioinfo/galaxy/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /usr/local/bioinfo/galaxy/galaxy_dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /usr/local/bioinfo/galaxy/galaxy_dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /usr/local/bioinfo/galaxy/galaxy_dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /usr/local/bioinfo/galaxy/galaxy_dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:7070$1 [P] And these ones to universe_wsgi.ini : [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy [app:main] filter-with = proxy-prefix cookie_path = /galaxy I face a problem with the history panel which always displays : "Your history is empty. Click 'Get Data' on the left pane to start >. Even if I upload Data, even if I log into galaxy. Here is an output of galaxy logs : 195.221.174.200 - - [13/Apr/2011:16:38:56 +0200] "GET /galaxy/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://marmadais.cirad.fr:7070/galaxy/root/tool_menu" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:2.0) Gecko/20100101 Firefox/4.0" galaxy.web.framework DEBUG 2011-04-13 16:39:04,250 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-04-13 16:39:04,251 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-04-13 16:39:04,251 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-04-13 16:39:04,251 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create galaxy.web.framework DEBUG 2011-04-13 16:39:04,251 Error: this request returned None from get_history(): http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create 195.221.174.200 - - [13/Apr/2011:16:39:04 +0200] "POST /galaxy/tool_runner/upload_async_create HTTP/1.1" 500 - "http://marmadais.cirad.fr:7070/galaxy/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:2.0) Gecko/20100101 Firefox/4.0" Error - <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'id' URL: http://marmadais.cirad.fr:7070/galaxy/tool_runner/upload_async_create File '/SATA/bioinfo/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/ errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/SATA/bioinfo/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.p y', line 80 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexcepti ons.py', line 632 in __call__ return self.application(environ, start_response) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 65 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/web/controllers/tool_runner.py' , line 212 in upload_async_create errors = tool.update_state( trans, tool.inputs, tool_state.inputs, kwd, update_only = True ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/tools/__init__.py', line 1192 in update_state value, error = check_param( trans, input, incoming_value, context ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/tools/parameters/__init__.py', line 56 in check_param value = param.from_html( value, trans, param_values ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 638 in from_html legal_values = self.get_legal_values( trans, context ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 808 in get_legal_values return set( dbkey for dbkey, _ in trans.db_builds ) File '/SATA/bioinfo/galaxy/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 695 in db_builds .filter_by( deleted=False, history_id=self.history.id, extension="len" ) AttributeError: 'NoneType' object has no attribute 'id' Any help welcome. Thankx.

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Re: [galaxy-dev] Error when trying to download workflow
by Jeremy Goecks 14 Apr '11

14 Apr '11

Hi Sarah, I created your workflow on my Galaxy instance and was able to export it successfully, so updating your Galaxy instance may solve your problem. If not, let us know and we'll take a closer look. Finally, please direct your questions to one of our mailing lists rather than individual galaxy developers for community and archival purposes; I've cc'd this one to galaxy-dev. Thanks, J. On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote: > Hi Jeremy, > > I encounter a similar error like the one already posted on the galaxy-dev list (http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html) when trying to download a workflow. > > Were you able to find a solution or are you still working on it? I attached a screenshot of the workflow (like you also requested on the list). Let me know if I can provide you with any additional details to help with the debugging. > > Best regards, > Sarah > > > > 10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] "GET /workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1" 500 - "http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322 file:///home/diehl/Pictures/Screenshot.png > Fedora/3.6.16-1.fc14 Firefox/3.6.16" > Error - <type 'exceptions.TypeError'>: 'WorkflowStep' object is unsubscriptable > URL: http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07 > File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ > app_iter = self.application(environ, start_response) > File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ > return self.application(environ, start_response) > File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ > return self.application(environ, start_response) > File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ > body = method( trans, **kwargs ) > File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 74 in decorator > return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) > File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1078 in export_to_file > stored_dict = self._workflow_to_dict( trans, stored ) > File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1571 in _workflow_to_dict > step['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) > TypeError: 'WorkflowStep' object is unsubscriptable > <Screenshot.png>

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Ratings on Tool Shed broken?
by Peter Cock 14 Apr '11

14 Apr '11

Hi all, I had wondered why none of the tools on the Galaxy Tool Shed had a rating, and had assumed it was just that so far no-one had bothered. I have a new theory, it doesn't work? I just viewed Brad's "BAM to BigWig" tool, clicked on "Tool Actions" then "Rate Tool", and got: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Can anyone reproduce this? I've tried a couple of other tools and the same thing happens. Thanks, Peter

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Output file naming / dataset's label
by Tanguy Le Carrour 14 Apr '11

14 Apr '11

Dear Galaxy Team, I started using Galaxy few months ago. I'm now setting up my first "real" workflows. I would like to keep the name of my input file through the various steps as dataset's label, maybe also modify it a bit, and finally give a "proper" name to the result file downloaded. A simple example: 1) date-sample_name.gff3 --[step1]-> date-sample_name-step1.tsv 2) date-sample_name-step1.tsv --[step2]-> date-sample_name-step1-step2.txt 3 download date-sample_name-step1-step2.txt I've seen that I can use the 'label' attribute in the tool config "data" tag to do so. But I don't know how to access the ${input.label} (?) and how to modify it. I doesn't stop me using my workflows, but it would definitely help my users not to get lost when they use them. Best regards, Tanguy Le Carrour -- Tanguy LE CARROUR Functional Genomics Center Zurich ETH Zurich / University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland

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