January 2013 - galaxy-dev - lists.galaxyproject.org

patch for workflow api
by Richard Park 30 Jan '13

30 Jan '13

Hi Guys, I've just updated to the latest galaxy-central and notice a problem when trying to export workflows via the api. In galaxy-central/lib/webapps/galaxy/api/workflows.py, I just need to add in an extra tab in lines 88 and 89, the patch is below. #### PATCH #### using hg diff diff -r 43fa4cb72e0f lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py Wed Jan 30 13:49:43 2013 -0500 +++ b/lib/galaxy/webapps/galaxy/api/workflows.py Wed Jan 30 14:43:46 2013 -0500 @@ -85,8 +85,8 @@ 'type': step.type, 'tool_id': step.tool_id, 'input_steps': {}} - for conn in step.input_connections: - steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, + for conn in step.input_connections: + steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, 'step_output': conn.output_name} item['steps'] = steps return item Could someone add this simple fix? I'd really appreciate it. Please let me know if I should be submtting a patch or pull request somewhere else. thanks, Richard

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Wiki reset password's email never arrives
by Carlos Borroto 30 Jan '13

30 Jan '13

Hi, I need help recovering my Galaxy Wiki password. I enter my information and I get the message about my account existing and an email was sent, but I never receive this email. Thanks, Carlos

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maximum recursion depth exceeded while calling a Python object
by Liisa Koski 30 Jan '13

30 Jan '13

Hi, I'm running a local instance of Galaxy and no matter what tool I run I get the following error: Error executing tool: maximum recursion depth exceeded while calling a Python object In the log file: galaxy.tools ERROR 2013-01-25 14:06:54,375 Exception caught while attempting tool execution: Traceback (most recent call last): File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1776, in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 2103, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/Galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py", line 203, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/Galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 1161, in get_converted_dataset new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=False ).values()[0] File "/Galaxy/galaxy_dist/lib/galaxy/datatypes/data.py", line 467, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 2103, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/Galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py", line 203, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/Galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 1161, in get_converted_dataset new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=False ).values()[0] File "/Galaxy/galaxy_dist/lib/galaxy/datatypes/data.py", line 467, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 2103, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/Galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py", line 203, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/Galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 1161, in get_converted_dataset new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=False ).values()[0] File "/Galaxy/galaxy_dist/lib/galaxy/datatypes/data.py", line 467, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 2103, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) thousands of lines here...ending with... File "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 760, in _make_proxy selectable.columns.add(c) File "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/expression.py", line 1668, in add self[column.key] = column File "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/expression.py", line 1671, in __setitem__ if key in self: File "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/expression.py", line 1702, in __contains__ return util.OrderedProperties.__contains__(self, other) File "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/util.py", line 652, in __contains__ return key in self._data RuntimeError: maximum recursion depth exceeded while calling a Python object Any help would be much appreciated, Thanks in advance, Liisa

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rerun tool in a workflow
by Hagai Cohen 30 Jan '13

30 Jan '13

Hi, is it possible that when I rerun a tool it will also rerun the tools that depends on it?

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Different behavior of select tag in the tool configuration file when the number of options is different.
by Luobin Yang 30 Jan '13

30 Jan '13

Hi, I have a 'select' tag in a tool's XML file, I would like to have a default option, which is choosing nothing. So the drop down menu of the web interface will be empty and when a user clicks the drop down menu, the list contains an empty entry with other options. So I basically have an option tag like the following <option value=""></option> together with other options. This works fine when I have up to 19 options including the default options. A user can submit the job without selecting any options and the program will use the default option. However, when the number of options exceeds 20, then drop down menu of the web interface displays "Click to Select or Search" instead of empty. And the user has to select one of the options in order to submit the job, otherwise, a question mark is displayed in the drop down menu and then an error message shows up under the drop down menu with the message "An invalid option was selected, please verify". Why the behavior changed when there are 20 options or more for a drop down menu? Thanks, Luobin

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extract DNA sequences
by Solorzano, Eleanne 30 Jan '13

30 Jan '13

Hi, I am trying to extract my sequences from a fasta file in my galaxy account based on the start and end positions of a gff file. However, this is not working here. How do I specify that the strands I am extracting are in the fasta file in my account in Galaxy? Should I be using another tool, please? Thank you. Eleanne

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Reloading tool's configuration not working
by Joachim Jacob |VIB| 30 Jan '13

30 Jan '13

Hi, In the 'Admin' menu, reloading a tool's xml file does not update the tool's interface. Thanks for any assistance, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Best way to work with one directory and many files as 1 input
by Pierre Pericard 30 Jan '13

30 Jan '13

Hi all, We've just added some new tools based on R scripts to our local Galaxy instance. Most of these tools need to work at the root of the directory containing the input files (up to hundreds of XML files) spread among two or more sub-directories. The directory structure need to be kept since the R tools recursively search for files and use the subdirectories names as classes. To solve this problem we added a "dummy" datatype to our instance so we can upload the input directory as a zip file without Galaxy decompressing it. <datatype extension="dummy_zip" type="galaxy.datatypes.data:Data" mimetype="application/zip" display_in_upload="true" subclass="true" /> However, since our tools can be runned as a workflow and that most of them need this input directory we need to unzip it with R in the job working directory for each tool (about 5 times for the entire workflow). Furthermore, this solution doesn't seem very "clean" if we want to share our tools via the ToolShed. Is there a smart way to handle this kind of input directory that can be achieved with Galaxy default datatypes and/or that doesn't require to unzip a file each time we use a tool ? Any update on a behavior change about zip files (http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-June/005631.html) ? Thanks in advance for any input, Pierre -- Pierre Pericard IE CDD - Projet Peptisan Service Informatique et Bio-informatique (SIB) Station Biologique de Roscoff CNRS-UPMC Place Georges Teissier CS 90074 29688 Roscoff CEDEX FRANCE http://abims.sb-roscoff.fr/

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Re: [galaxy-dev] Reloading tool's configuration not working
by Joachim Jacob |VIB| 30 Jan '13

30 Jan '13

Unfortunately, no. Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 01/30/2013 10:56 AM, Peter Cock wrote: > On Wed, Jan 30, 2013 at 9:54 AM, Joachim Jacob |VIB| > <joachim.jacob(a)vib.be> wrote: >> Hi, >> >> >> In the 'Admin' menu, reloading a tool's xml file does not update the tool's >> interface. >> >> >> Thanks for any assistance, >> >> Joachim > I had a 'funny' recently where I had to do the xml reload twice, then it worked. > Same for you? > > Peter > >

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workflows stop prematurely
by mark.rose＠syngenta.com 29 Jan '13

29 Jan '13

Hi All On my local install of galaxy I'm having problems executing workflows. I will upload data into a new history and then select to run a saved workflow. This initiates fine but, after the completion of a variable number of steps, the workflow just stops after the successful completion of a step. No errors appear in the web interface and all I can see in the paster.log is something like 90 HTTP/1.1" 200 - "http://127.0.0.1:8081/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" 127.0.0.1 - - [28/Jan/2013:12:29:07 -0400] "GET /api/histories/82b264d8c3d11790 HTTP/1.1" 200 - "http://127.0.0.1:8081/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" galaxy.jobs.runners.local DEBUG 2013-01-28 12:29:08,621 execution finished: python /home/rosema1/Projects/galaxy-dist/tools/fastq/fastq_trimmer_by_quality.py '/home/rosema1/Projects/galaxy-dist/database/files/000/dataset_590.dat' '/home/rosema1/Projects/galaxy-dist/database/files/000/dataset_592.dat' -f 'sanger' -s '5' -t '1' -e '53' -a 'mean' -x '0' -c '>=' -q '20.0' galaxy.jobs DEBUG 2013-01-28 12:29:08,838 Tool did not define exit code or stdio handling; checking stderr for success galaxy.tools DEBUG 2013-01-28 12:29:09,135 Error opening galaxy.json file: [Errno 2] No such file or directory: '/home/rosema1/Projects/galaxy-dist/database/job_working_directory/000/418/galaxy.json' galaxy.jobs DEBUG 2013-01-28 12:29:09,439 job 418 ended galaxy.jobs DEBUG 2013-01-28 12:29:10,041 (420) Working directory for job is: /home/rosema1/Projects/galaxy-dist/database/job_working_directory/000/420 galaxy.jobs.handler DEBUG 2013-01-28 12:29:10,042 dispatching job 420 to local runner galaxy.jobs.handler INFO 2013-01-28 12:29:10,200 (420) Job dispatched galaxy.jobs.runners.local DEBUG 2013-01-28 12:29:10,385 Local runner: starting job 420 galaxy.jobs.runners.local DEBUG 2013-01-28 12:29:10,759 executing: python /home/rosema1/Projects/galaxy-dist/tools/fastq/fastq_filter.py /home/rosema1/Projects/galaxy-dist/database/files/000/dataset_592.dat /home/rosema1/Projects/galaxy-dist/database/job_working_directory/000/420/tmph0Ll2V /home/rosema1/Projects/galaxy-dist/database/files/000/dataset_594.dat /home/rosema1/Projects/galaxy-dist/database/job_working_directory/000/420/dataset_594_files 'sanger' 127.0.0.1 - - [28/Jan/2013:12:29:12 -0400] "GET /api/histories/82b264d8c3d11790 HTTP/1.1" 200 - "http://127.0.0.1:8081/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" 127.0.0.1 - - [28/Jan/2013:12:29:12 -0400] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://127.0.0.1:8081/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" 127.0.0.1 - - [28/Jan/2013:12:29:12 -0400] "GET /api/histories/82b264d8c3d11790/contents?ids=3da459a26c8f00b4%2C736af8f0a76a2e71 HTTP/1.1" 200 - "http://127.0.0.1:8081/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" 127.0.0.1 - - [28/Jan/2013:12:29:16 -0400] "GET /api/histories/82b264d8c3d11790 HTTP/1.1" 200 - "http://127.0.0.1:8081/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" Though I seem to see this even when a step completes and the workflow proceeds. Moreover, if I then begin executing the next steps in the workflow, they work, but create new entries in the history. So, some questions: Why is this happening and what can I do to get workflows to run to completion? Also, is it possible to reinitiate the workflow from the premature stopping point without having to launch each step individually and point each at new inputs rather than the ones dictated in the workflow? Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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