August 2014 - galaxy-dev - lists.galaxyproject.org

filtering a <param> of type 'data' so only one type is available
by Dan Tenenbaum 24 Oct '14

24 Oct '14

Hi, I have a tool wrapper with a <param> of type="data". Currently, this renders as a text box with a drop down list that has 52 items in it (the number of things I have in my history, I guess). I'd like to filter this list so that only some items in the history (in my case any item whose name ends with '.rda') are shown in this dropdown. It seems like maybe the 'format' parameter to the 'param' tag is what I want, but: 1) I tried format="rda" and that didn't seem to change anything. 2) "rda" is not in the datatypes.conf file which the documentation suggests is required? (.rda is an extension used for serialized R objects.) The tool I'm working on only accepts rda files as input and the reason I'm asking for this is that it is all too easy to accidentally feed it a file of some other type. If the dropdown could be filtered so that only items which will work with the tool are shown, that would be great. Is there a way to do that? Thanks, Dan

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IE 11 issues
by Sajdak, Doris 24 Sep '14

24 Sep '14

We are having issues with using Galaxy in Internet Explorer 11 (these work fine in Chrome & Firefox). 1. The jobs queued and history doesn't display unless you refresh the browser window. Clicking the history reload icon doesn't work. 2. If I click to edit something in the history, the tabs aren't clickable. Attributes are displayed but I can't click on Convert Format, Datatype, or Permissions. Anyone else having this problem? I apologize if this information is documented somewhere but I was unable to find it. Thank you for your assistance, Dori ********************************** Dori Sajdak Senior Systems Administrator State University of NY at Buffalo Center for Computational Research 701 Ellicott St Buffalo, NY 14203 Phone: (716) 881-8934 Fax: (716) 849-6656 Web: http://ccr.buffalo.edu **********************************

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Workflow param error leads to template error
by Paul-Michael Agapow 19 Sep '14

19 Sep '14

Looking for pointers on what might be causing this problem: A user had a moderately complicated workflow that when run under certain parameter values results in a traceback that ends: Module workflow_run_mako:232 in render_body >> for ic in oc.input_step.module.get_data_inputs(): AttributeError: 'WorkflowStep' object has no attribute 'module' After some puzzling, I realized one of the parameters was outside the allowed range (a max on an integer param) and that Galaxy was trying to render "run.mako" flagging up the error but erroring out. Why Galaxy tries to call this non-existent member is unclear to me. Any insight or places I should start exploring? Galaxy version: various (started with an 6-month old one, upgraded to latest production to see if it would fix error, it didn't) Hosting OS: CentOS 6 ------ Paul Agapow (paul-michael.agapow(a)hpa.org.uk) Bioinformatics, Health Protection Agency (UK) ************************************************************************** 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 by Symantec.Cloud, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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BAM to SAM tool no way to get an unsorted SAM?
by Alistair Chilcott 10 Sep '14

10 Sep '14

Hello all, My users are trying to use a tool called bismark and it requires an unsorted SAM file for one of its steps Previous steps produce BAM files so we would like to include the tool BAM-to-SAM as a step in the workflow unfortunately it seems to be set to sort by default and there is no way to alter this behaviour. Is there another tool that would convert a BAM to a SAM without sorting it or can the BAM-to-SAM tool be altered to include a checkbox for an unsorted result? Regards, Alistair

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Examples of Galaxy tools in the toolsheds that install and run JAR files properly?
by Melissa Cline 04 Sep '14

04 Sep '14

Hi folks, I'm attempting something that should be straightforward, but it's not. I have a tool that runs a JAR file, which I have bundled with the tool. I simply want to run the JAR file. And to paraphrase Thomas Edison, I've tried several thousand things that do not work (at least for me), from setting the JAVA_JAR_PATH environment variable in the tool_dependencies.xml file to trying to copy the JAR file into the tool-data/shared/jars subdirectories (which is the closest thing I've got to working). So, at long last I'm doing the sensible thing and looking for one simple working example that I can use as a template. Who can suggest a good toolshed tool (either main or test) that involves running its own JAR file, and that works? Thanks! Melissa

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Concept for a Galaxy Versioned Fasta Data Retrieval Tool
by Dooley, Damion 03 Sep '14

03 Sep '14

We are about to implement a fasta database (file) versioning system as a Galaxy tool. I wanted to get interested people's feedback first before we roll ahead with the prototype implementation. The versioning system aims to: * Enable reproducible research: To recreate a search result at a certain point in time we need versioning so that search and mapping tools can look at sequence reference databases corresponding to a particular past date. This recall can also explain the difference between what was known in the past vs. currently. * Reduce hard drive space. Some databases are too big to keep N copies around, e.g. 5 years of 16S, updated monthly, is say, 670Mb + 668Mb + 665Mb + .... But occasionally we want to access past archives fairly quickly. * Integrate database versioning into Galaxy without adding a lot of complexity. A bonus would be to enable the efficient sharing of version databases between computers/servers. The solution we think would work centres around a "Versioned Data Retrieval" tool (draft image attached) that would work as follows: 1) User selects from a list of databases provided by "Shared Data > Data Libraries > Versioned Data". - Each database has a master file that keeps its various versions as a list of time-stamped insert/delete transactions of key (fasta id) value (description & sequence) pairs. - Each master file is managed outside of galaxy via a triggered process on regular fasta file imports from data sources like NCBI or other niche sources. - We're expecting, due to the nature of fasta archived sequence updates, that our master file would only be about 1.1x the latest version in size (uncompressed). 2) User enters date / version id to retrieve (validated) 3) If a cached version of that database exists, it is linked into user's history. 4) Otherwise a new version of it is created, placed in cache, and linked into history. - The cached version itself then shows up as linked data under a Data Library > Versioned Data subfolder. 5) User can select preconfigured workflow(s) to execute on the selected retreived fasta file to regenerate any database products they need. - Workflow output data would also be cached in the same way the fasta data is - by linking the Galaxy Data Library to it. - Workflow execution will be skipped if end data already exists in cache. - Simple makeblastdb or bowtie-build commands, or more specific workflows that include dustmasker etc can be implemented. Does this sound attractive? We're hoping such a vision could handle Fasta databases from 12mb to e.g. 200Gb (probably requires makeblastdb in parallel at that scale). Preliminary work suggests this project is doable via the Galaxy API without galaxy customization - does that sound right?! Feedback really appreciated! Regards, Damion Dooley Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada

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"when else" in <conditional> ? RE: refresh_on_change : is this a valid attribute? Any other ideas/options??
by Lukasse, Pieter 03 Sep '14

03 Sep '14

So I need to refresh on change....I see that if I have a conditional item in my form, this causes a refresh of the page and a (re)evaluation of my dynamic_options methods....so I could misuse this "feature". However, it seems that when I have a <conditional> I must have a <when> entry for every item in my select box. There is no "when else" option? Thanks, Pieter From: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: woensdag 27 augustus 2014 22:37 To: galaxy-dev(a)lists.bx.psu.edu Subject: [galaxy-dev] refresh_on_change : is this a valid attribute? Any other ideas/options?? Hi, I'm trying to get a wrapper from someone else working and I found this "refresh_on_change" attribute in his select boxes which are filled using the dynamic_options feature: <param name="col_type" type="select" label="Select column type" refresh_on_change="true" display="radio" dynamic_options='get_column_type(library_file)' help="" /> <param name="polarity" type="select" label="Select polarity" refresh_on_change="true" display="radio" dynamic_options='filter_column(library_file,col_type)' help="" /> ... When searching the documentation/wiki I do not find a reference to this, but it would be a nice option to have ;) Question: is there any way I can force a refresh when the user selects another option from such a select box. As you can see in the example above, this is needed because the next select box has its dynamic options built up by a function that takes the value from the previous select (col_type - highlighted above) as an input parameter. Currently this tool only works by showing each select in its own <page> , which is a deprecated option and prevents the tool from being used in a workflow... :( Thanks for your help! Best regards, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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testing the visualization plugins
by Hans-Rudolf Hotz 01 Sep '14

01 Sep '14

Hi As part of my upgrade/testing work, I am looking at the visualization plugins. In a new galaxy installation ("latest_2014.08.11"), they (ie 'Charts', 'Scatterplot', and 'Trackster') seem to work fine. All I have done was: - I defined the visualization_plugins_directory in the universe_wsgi.ini file If I comment-out this line, I only get trackster, when I click on the icon which looks like a bar-plot Next, I have tried it on our development server (after I have upgraded from "release_2014.04.14" to "latest_2014.08.11"). I changed the universe_wsgi.ini file. I the logs I get: galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,639 VisualizationsRegistry, loaded plugin: charts galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,641 VisualizationsRegistry, plugin load failed or disabled: ./config/plugins/visualizations/circster. Skipping... galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,655 VisualizationsRegistry, loaded plugin: graphview galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,657 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,675 VisualizationsRegistry, loaded plugin: scatterplot galaxy.web.base.pluginframework WARNING 2014-08-27 09:43:45,677 VisualizationsRegistry, plugin load failed or disabled: ./config/plugins/visualizations/sweepster. Skipping... galaxy.web.base.pluginframework INFO 2014-08-27 09:43:45,679 VisualizationsRegistry, loaded plugin: trackster wrt to 'Charts', 'Scatterplot', and 'Trackster', this looks fine to me. However, if I hoover over the bar-plot icon, "Visualize in Trackster" pops up (instead of just "Visualize"), and when I click on it I get straight to the Trackster page, where, I am asked to define the Browser name and the Reference genome. No links for 'Charts' and 'Scatterplot'. On the other hand, the plug in infrastructure seems to work: If I change ~/config/plugins/visualizations/trackster/config/trackster.xml I see the effects, ie if I change result_type="datatype">data.Data< to result_type="datatype">interval.Interval I can restrict the visualization to only the interval data. Somehow, I am running a mixture of the 'old' and the 'new' visualization set-up ? Has anyone seen similar problems when testing the new plug in infrastructure on an old/upgraded Galaxy installation Thank you very much for any hints and help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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error with multi dataset tool run
by Robert Baertsch 01 Sep '14

01 Sep '14

I submitted 13 fastq files to tophat2 using DRMAA and got this error. Is it fatal? BTW: This is a super cool feature. I’m running the following version of galaxy-dist. changeset: 14212:91547729ffde branch: stable tag: tip user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Aug 29 14:00:23 2014 -0400 summary: Update tag latest_2014.08.11 for changeset ea12550fbc34 -Robert There were errors setting up 2 submitted job(s): Error executing tool: (OperationalError) database is locked u'UPDATE history_dataset_association SET update_time=?, name=?, blurb=? WHERE history_dataset_association.id = ?' ('2014-08-30 23:14:44.683957', 'Tophat2 on data 7: insertions', 'queued', 137) Error executing tool: (OperationalError) database is locked u'UPDATE dataset SET update_time=?, state=? WHERE dataset.id = ?' ('2014-08-30 23:15:57.204718', 'queued', 446)

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Problem Running TopHat2
by Kevin 30 Aug '14

30 Aug '14

Hello All, I am running a Galaxy instance on Linux and have installed tools from the Galaxy Main Tool Shed. However, whenever I run TopHat2, the program is unable to complete the job before I get the following error message: Traceback (most recent call last): File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found So far, I have made sure that the samtools do appear to be installed since they can be found listed under "Managed Installed Tool Shed Repositories". Is it possible that they were installed incorrectly? Any help is much appreciated. Thanks for taking the time to read this, Kevin Chang

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