- galaxy-dev - lists.galaxyproject.org

Blast+: new feature filter/mask... by taxid before job in one task
by Berner, Thomas 26 Feb '14

26 Feb '14

Hi guys, We recently installed NCBI BLAST + to our local Galaxy instance and now we need to provide the possibility to filter/mask ... by taxon id (taxid) using the command line option (-window_masker_taxid) of BLAST (cf. http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the job will be performed in one task. However searching in the documentation and the mailing list, I did not find anything about this. So it would be great to provide the possibility to subselect by taxid (e.g. NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by changing the BLAST integration. We believe this could be of common interest. It would be great if anybody could comment on this. Thanks a lot, Thomas

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using svg foreignObject tags can circumvent html sanitization
by Tobias Sargeant 26 Feb '14

26 Feb '14

In experimenting with how we could embed javascript/unsanitized html in tool output we came across the following method. Given that the current default is to disallow such activities, we thought it might be useful to bring it to your attention. The attached file provides an example, which, when uploaded to a history and viewed produces a popup on the current stable release of galaxy (local install and https://usegalaxy.org) Cheers, Tobias Sargeant.

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Parallelism-enabled NCBI BLAST+ blastn does not appear to complete
by Sanka, Ravi 26 Feb '14

26 Feb '14

Greetings, We are trying to enable job-splitting and merging on our Galaxy blast tools. We set the following parameters in the universe_wsgi.ini: use_tasked_jobs = True local_task_queue_workers = 2 Then we executed the tool "NCBI BLAST+ blastn" (from devteam's NCBI BLAST+) on a query set of 10,000 sequences. The tool's xml has the following parallelism tag: And as expected, the job was split into 10 tasks (IDs 0-9), each one with 1000 sequences. Four tasks started running simultaneously. Those four tasks have completed, but now there is no indication that the other 6 tasks have begun running, and the job on the GUI is still in the yellow-state in History. It has been nearly an hour, and still no sign of those tasks or any job running. What could be the cause of this? ---------------------------------------------- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 ----------------------------------------------

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local toolshed with remote-user=true and require-user=falase
by Langhorst, Brad 26 Feb '14

26 Feb '14

Has anyone set up a local toolshed with external authentication? Is this expected to work? I have external auth working, but tools cannot be installed (403 forbidden) unless I turn of authentication. If i turn on remote-auth, i have to configure the webserver to ask for credentials otherwise i get an error page. It would make sense to have the webserver request credentials only for requests to a login page, but I don’t see how to do that. For now I’ve just turned off remote-auth. Brad -- Brad Langhorst, Ph.D. Applications and Product Development Scientist

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Cufflinks doesn't stop
by Federico Zambelli 26 Feb '14

26 Feb '14

Hi, something strange happens with Cufflinks in our Galaxy server. When a user deletes a running Cufflinks job in fact the associated Cufflinks process(es) are not terminated. Apart from unneccessary CPU usage, this prevents other jobs from starting if the max jobs limit has been already reached by the user. This happens only with Cufflinks, Cuffcompare for comparison behaves just fine. Best, F. -- ============================================ Federico Zambelli, Ph.D. Bioinformatics, Evolution and Comparative Genomics Lab Dept. of Biosciences University of Milano - Italy What can be asserted without proof can be dismissed without proof. ============================================

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You do not have permission to add datasets to 1 requested histories.
by Shrum, Donald C 26 Feb '14

26 Feb '14

I have galaxy running as the galaxy user on a virtual machine. I've enabled ldap authentication and the galaxy software is running on our HPC file system. I've created a scratch folder on our HPC file system for users to use to upload data from a filesystem path. I'm able to upload a data file but when I attempt to import the data into my 'current history' which I think I need to do in order to run a job using this data... I get a message that reads 'You do not have permission to add datasets to 1 requested histories.' I've tried looking at paster.log to no avail. Is there a better log to use... any help would be greatly appreciated. Thanks, Donny FSU Research Computing Center

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contributing patches to toolshed repos...
by Langhorst, Brad 25 Feb '14

25 Feb '14

What’s the right way to contribute additions to other people’s repos? I have extended the picard wrappers to support the rna-seq metrics and downsample sam tools, but I don’t want to start a new repo just for these. I have attached the output from hg outgoing -p in case that’s useful

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MAF Import Error
by Doan, Ryan 25 Feb '14

25 Feb '14

Hello, I am trying to import an large MAF file (gzipped at 5gb, unzipped =60gb). When I import the file, I get the following message upon completion: "An error occurred setting the metadata for this dataset. You may be able to set it manually or retry auto-detection" However, when I open setting and try auto-detection, I continue to get the error. Is this an issue with the file size (I can upload smaller MAFs of 20Gb without a problem)? I am certain the file is not corrupt since it was downloaded through FTP from UCSC (also tried directly importing from UCSC into galaxy, but got the same error). Thanks, Ryan

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Error when installing package_galaxy_utils
by Sarah Diehl 25 Feb '14

25 Feb '14

Hi everyone, I just updated our local Galaxy installation to the latest dist version and also did the tool migration steps (./scripts/migrate_tools/0009_tools.sh). However, the package galaxy_utils gave me an error and I don't have the slightest idea what happened. So any help to figure out the issue is greatly appreciated! Thanks, Sarah ############################################# export PYTHONPATH=$PYTHONPATH:/galaxy/galaxy_data/tools/galaxy_sequence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7/lib/python && python setup.py install --home /galaxy/galaxy_data/tools/galaxy_seq uence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7 STDERR Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.38.tar.gz Extracting in /tmp/tmpo9Zxdz Now working in /tmp/tmpo9Zxdz/distribute-0.6.38 Building a Distribute egg in /galaxy/galaxy_server/database/tmp/tmp-toolshed-mtd00x35_/galaxy_sequence_utils-1.0.0 /galaxy/galaxy_server/database/tmp/tmp-toolshed-mtd00x35_/galaxy_sequence_utils-1.0.0/distribute-0.6.38-py2.7.egg error: site.py: Resource temporarily unavailable #############################################

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Optional multiple file selectors,
by Peter Cock 25 Feb '14

25 Feb '14

Hi John, As you noticed (and posted on Twitter), I've just tweaked the NCBI makeblastdb wrapper on GitHub to use a multiple file picker instead of a repeat: https://github.com/peterjc/galaxy_blast/commit/858bf541a828644ea6461b20b687… That seems to be working fine in human testing (although not on the functional side). I've also just tried this for the masking files - but ran into a problem. Here the masks are optional, and I want the default to be no mask: https://github.com/peterjc/galaxy_blast/commit/e1bcb24ac24613395a0fe327c54c… This works fine from the user interface perspective: <param name="input_file" type="data" multiple="true" optional="false" format="fasta" label="Input FASTA files(s)" help="One or more FASTA files" /> This requires at least one file, although a confusing red error message is given if none is selected: "History does not include a dataset of the required format / build" <param name="mask_data_file" type="data" multiple="true" optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary" label="Optional ASN.1 file(s) containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> This does not require a file, and defaults to selecting a new dummy entry "Selection is Optional". This is presumably intended as a visual cue - but it means you can do weird things like picking a read file and the dummy entry, or no entries. Neither allows me to proceed, instead on pressing execute I get a red error on a new page: Error executing tool: 'NoneType' object has no attribute 'file_name' galaxy.tools ERROR 2014-02-25 14:02:47,844 Exception caught while attempting tool execution: Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line 1916, in __handle_tool_execute _, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line 2424, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/actions/__init__.py", line 287, in execute data.name = self.get_output_name( output, data, tool, on_text, trans, incoming, history, wrapped_params.params, job_params ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py", line 26, in params self.wrap_values( self.tool.inputs, params, skip_missing_values=not self.tool.check_values ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/parameters/wrapped.py", line 51, in wrap_values name=input.name ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line 215, in __init__ list.__init__( self, map( to_wrapper, datasets ) ) File "/mnt/galaxy/galaxy-central/lib/galaxy/tools/wrappers.py", line 209, in to_wrapper real_path = dataset.file_name AttributeError: 'NoneType' object has no attribute 'file_name' Any thoughts? Is zero files a little tested corner of the multiple file support? If I have a suitable masking file in my history, and I select it, the tool runs fine. Thanks, Peter

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