galaxy-dev November 2011

galaxy-dev@lists.galaxyproject.org

83 participants
157 discussions

ImportError: No module named galaxy
by Oren Livne 07 Nov '11

07 Nov '11

Dear All, I am running the example_watcher_folder.py API script and it intermittently fails to run a workflow on a file dropped into the import directory (the file is imported and the workflow starts running, but its jobs hang or fail). Galaxy uses a condor dramaa job runner. When I look at the galaxy script being run by condor, it sets the PYTHONPATH and then executes the following command, which also fails at the command line. galaxy@vm-debian:~/galaxy-dist$ python /home/galaxy/galaxy-dist/tools/filters/sorter.py --input=/tmp/galaxy/datafiles/000/dataset_105.dat --out_file1=/tmp/galaxy/datafiles/000/dataset_106.dat --column=7 --style=num --order=DESC Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/filters/sorter.py", line 15, in <module> from galaxy import eggs ImportError: No module named galaxy How can I resolve this error? I would like to be able to test such commands at the command line, as well as ensure that galaxy workflows run reliably. Thanks, Oren

2 3

Best documentation for parallel cluster support in Galaxy
by Arthur Goldberg 07 Nov '11

07 Nov '11

Hi Where's the best documentation for parallel cluster support in Galaxy, please? BR A -- Senior Research Scientist Computational Biology Memorial Sloan-Kettering Cancer Center cBio Cancer Genomics Portal <http://www.cbioportal.org/>

2 1

last hurdle
by Robert Day 07 Nov '11

07 Nov '11

Hi, Sorry to bother you guys with such a simple thing. I'm quite new to the terminal and command line etc. so downloading and getting Galaxy running on my PC was a voyage of discovery! Anyhow, I have it, it's alive.......... just can't get any data in! Have made myself an Admin User to create a data library, I point the importer at the files and it starts but never stops and remains at 0bytes. Have I forgotten to set something up? Surely I can just dump all my files in a folder in the right place and go get it when I need it. Can't seem to find an idiots guide for setting this up for a local install (just me and my computer). Any pointers or helpful threads would be great. Cheers Rob Sent from my PC

3 2

making data libraries from database tables
by James Ireland 07 Nov '11

07 Nov '11

Greetings! I would like to expose data I have in a relational database as a data library in Galaxy. I would really like to do this without Galaxy having to make a local copy of the data to the file system. Is this possible and could you point me to any code examples and/or documentation? I'm sure this must be covered somewhere in the documentation or mailing list, but I haven't been able to find it. Thanks for your help! -James -- J Ireland www.5amsolutions.com | Software for Life(TM) m: 415 484-DATA (3282)

2 1

Workflow output selection bug
by Chorny, Ilya 07 Nov '11

07 Nov '11

I think there is another bug in the output selection of the workflows. If I select only certain number of outputs (by selecting the orange star) to be show in history following a workflow and then edit the workflow to show more outputs, the number of outputs in the history does not change and the history only shows the number of originally selected outputs. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

1 0

Error when clicking on published workflows
by Chorny, Ilya 07 Nov '11

07 Nov '11

URL: http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test Module paste.exceptions.errormiddleware:143 in __call__ >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> environ, self.app) Module paste.wsgilib:539 in intercept_output >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:111 in __call__ >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> body = method( trans, **kwargs ) Module galaxy.web.controllers.workflow:221 in display_by_username_and_slug >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) Module galaxy.web.framework:718 in fill_template_mako >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> return template.render( **data ) Module mako.template:296 in render >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> callable_(context, *args, **kwargs) Module _base_panels_mako:100 in render_body >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> __M_writer(unicode(self.center_panel())) Module _display_base_mako:219 in render_center_panel >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> __M_writer(unicode(self.render_content())) Module _display_base_mako:179 in render_render_content >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> __M_writer(unicode(self.render_item( item, item_data ))) Module workflow_display_mako:136 in render_render_item >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> __M_writer(unicode(do_inputs( tool.inputs, step.state.inputs, "", step ))) Module workflow_display_mako:91 in do_inputs >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> return render_do_inputs(context,inputs,values,prefix,step,other_values) Module workflow_display_mako:216 in render_do_inputs >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> __M_writer(unicode(do_inputs( input.inputs, repeat_values[ i ], prefix + input.name + "_" + str(index) + "|", step, other_values ))) Module workflow_display_mako:181 in do_inputs >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> return render_do_inputs(context,inputs,values,prefix,step,other_values) Module workflow_display_mako:246 in render_do_inputs >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> __M_writer(unicode(row_for_param( input, values[ input.name ], other_values, prefix, step ))) Module workflow_display_mako:179 in row_for_param >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> return render_row_for_param(context,param,value,other_values,prefix,step) Module workflow_display_mako:300 in render_row_for_param >> <http://ussd-dev-swim02.illumina.com/galaxy2/u/ichorny/w/test> if isinstance( param, DataToolParameter ): TypeError: isinstance() arg 2 must be a class, type, or tuple of classes and types Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

2 5

history name and tool number in XML tool definition
by Marc Sturm 07 Nov '11

07 Nov '11

Hello everyone, I have a question how to access the history name and tool number (the number displayed in the history) in the XML tool definition file. We want all tools of a history to log to a common log file using the tool number to distinguish the different tools. Thus, I'd like to do something similar to this: <tool id="custom_dummy" name="dummy"> <command interpreter="php" >dummy.php -log ${history_name}.log -log_id ${tool_number}</command> . </tool> Is there a way to do this? I could not find it using the documentation or the mailing list archive. Best wishes, Marc

1 0

Ucsc bigbed display tool does not show up on local installation
by Jeremy Villalobos 05 Nov '11

05 Nov '11

Hello: The display tool for UCSC that comes with the local installation package does not work. uploading a bigbed file (from the test-data that comes with the package) does not trigger the webapp to show an option to view the file using UCSC's viewer. How do I enable this ? To reproduce the issue, simply download galaxy using mercurial. change the host address to 0.0.0.0. and load the bigbed file from the test-data directory. Once the file uploads, the user should expect to see a display tool added to the files description (on the right), but nothing is shown. Thanks Jeremy UNCC

2 2

Clusters, Runners, and user credentials
by Lloyd Brown 04 Nov '11

04 Nov '11

I'm a systems administrator for an HPC cluster, and have been asked by a faculty member here to try to get galaxy to work on our cluster. Unfortunately, there are one or two outstanding questions that I can't seem to find the answer to, and I'm hoping someone here can help me out. In particular, is galaxy, and the PBS runner specifically, capable of submitting jobs under specific user names? Essentially, if I set up galaxy to push jobs to our cluster, will they all show up under one user credential (eg. the "galaxy" user), or can we set it up so that the user logged into galaxy, is used to submit the job? This one is kindof a show-stopper, since our internal policies require that all jobs have a specific user credential, with one person per username. Thanks, Lloyd -- Lloyd Brown Systems Administrator Fulton Supercomputing Lab Brigham Young University http://marylou.byu.edu

5 10

fastx reverse compliment failed - gzip: stdout: Broken pipe
by Lucinda Lawson 04 Nov '11

04 Nov '11

I'm reposting over here from the user side, since this is a local instance, and it was recommended. Hi all, We are running Galaxy on an Ubuntu 11.10 computer (5 TB, stripped, etc.). We are assembling a small genome (110 Gb). Our dataset isn't directly uploaded, but is accessed from a directory (if that matters). Everything went fine through the FASTQ Groomer, but when we ran Reverse-Compliment, we got the following error: fastx_reverse_complement: writing quality scores failed: File too large gzip: stdout: Broken pipe Any help that you might have would be greatly appreciated! Thanks! As a follow up, the file that we're trying to reverse compliment is ~26 Gb. The files seem to work fine until 2.1 Gb. There is plenty of memory (we have 3.4 Tb free on this system) and it doesn't seem to be an issue with the permissions or partitions. I also made sure that the Gzip and connectors to perl are up to date. And I have set everything in ulimit to be unlimited (so there are no issues for Ubuntu for the file size creation). This is a local instance, btw, though I'm sure that's obvious... We were able to groom the files to create the 26Gb file that we want to work with, so it seems like the computer should be able to do all of this... Any thoughts?

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galaxy-dev November 2011