galaxy-dev June 2013

galaxy-dev@lists.galaxyproject.org

111 participants
189 discussions

transferring Trapnell et al programs into a one user instance of Galaxy
by Elwood Linney 17 Jun '13

17 Jun '13

Hello again, I guess I now realize why there is so much traffic on the user list about tools, and I also can guess that while the online directions for dealing with them are written well for those individuals familiar with administration a server or doing full time bioinformatics, but there are some of us computer numbskulls that need something like a Galaxy transfer booklet for computer idiots (biologists) to transfer what we want into a single user or single lab setup. I am hoping there is someone out there like myself who worked through the problem of transferring the Trapnell et al series of programs into a Mac Pro desktop, namely NGS: RNA Analysis 1) Tophat for Illumina tophat (1.3.3-1.4.0) with bowtie + bowtie indexes 2) Cufflinks cufflinks (1.3.0-2.1.1) 3) Cuffcompare cufflinks (1.3.0-2.1.1) 4) Cuffmerge cuffmerge (1.3.0-2.1.1) 5) Cuffdiff cuffdiff (2.1.0-2.1.1) I have transferred the galaxy framework in a work/galaxy-dist pathway unto a solid state drive of a 64gb ram mac that has 3 other 2tb drives and have gotten some valuable advice for transferring large datasets from the same computer via admin. For the next year at least my needs with be just the RNA analysis tools above. Any help will be greatly appreciated. My intention here is remove my contribution to the traffic on the online Galaxy, so some people should consider it a worthy cause Sincerely, Elwood Linney Professor of Molecular Genetics and Microbiology Duke University Medical Cener

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wiki surge protection broken
by Brian Craft 15 Jun '13

15 Jun '13

Followed a google result to the wiki, and got a "surge protection" warning: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Unless you're protecting from "surges" of 0.5 - 1 pages per hour, your surge protection is broken.

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docs for data_source.py, file type handling, etc.
by Brian Craft 15 Jun '13

15 Jun '13

I'm trying to add a data source that provides tarballs. Are there any docs for data_source.py, the data types registry, and so-forth? The data source docs seem to only cover the http callback mechanism. I'm trying to understand what happens after that: a json file is created with download params, data_source.py reads it and then overwrites it with the downloaded file, the registry is consulted for additional processing, which then gunzips the tarball. Gunzip isn't necessarily the right step. It might be better to tar-extract appropriate files and let galaxy know about them somehow. I can call data_source.py from a custom tool, and then handle the tar steps, but I don't know how to direct galaxy to the untarred files.

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nglims/services/python
by Lee Katz 15 Jun '13

15 Jun '13

Hi, I am running into an error that I bet has a simple solution. I would appreciate any help. Thanks. I am running Brad Chapman's LIMS extension locally on Ubuntu 12. I also installed it as a service under /etc/init.d/chapman-galaxy using contrib/galaxy.debian-init . It works when I run it directly (./run.sh --reload) When I run a version of Galaxy without nglims as a service, there is no error. When I run a version of Galaxy with nglims, not as a service (run.sh), there is no error. However, when I run the same version of Galaxy with nglims as a service, there is an error. I don't understand well enough what the difference is when I run it as a service to diagnose this problem. The lines leading to the error from the log file is below. Something to do with yaml not being loaded, but I know I installed python-yaml through aptitude. galaxy.web.framework.base DEBUG 2013-06-14 09:46:26,873 Enabling 'requests' controller, class: Requests galaxy.webapps.galaxy.controllers library_common galaxy.webapps.galaxy.controllers.library_common galaxy.web.framework.base DEBUG 2013-06-14 09:46:26,874 Enabling 'library_common' controller, class: LibraryCommon galaxy.webapps.galaxy.controllers nglims galaxy.webapps.galaxy.controllers.nglims Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run result = self.command() File "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/home/galaxy/bin/chapman-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 225, in loadobj return context.create() File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 188, in invoke filtered = context.next_context.create() File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/home/galaxy/bin/chapman-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/home/galaxy/bin/chapman-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 44, in app_factory webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) File "/home/galaxy/bin/chapman-dist/lib/galaxy/web/framework/__init__.py", line 274, in add_ui_controllers module = import_module( module_name ) File "/home/galaxy/bin/chapman-dist/lib/galaxy/util/backports/importlib/__init__.py", line 37, in import_module __import__(name) File "/home/galaxy/bin/chapman-dist/lib/galaxy/webapps/galaxy/controllers/nglims.py", line 24, in <module> import yaml ImportError: No module named yaml

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printing output from java tool in the middle pane in galaxy
by vijayalakshmi 15 Jun '13

15 Jun '13

Hi all, I am trying to integrate a tool written in java into galaxy. The java code will output a GUI window. I want to know how to output that window in the middle pane Thanks, VJ

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How to speed up submissions of workflows
by Thon Deboer 15 Jun '13

15 Jun '13

Hi, I am routinely running hundreds of pair-end sequencing runs and find that STARTING a workflow on all of these can easily take hours since it seems each workflow preparation takes about 3 minutes, so for doing 128 fastq pairs like this it will take over 3 hours just to get all workflows running.. Is there any way for me to speed up this process, maybe by adding more handlers (although I am suspecting the WEB server is the bottleneck here)? I already run 8 handlers but only one web server. I could loadbalance the webservers through my proxy server.Will that speed up the submissions or are we stuck with this linear process? Thanks, Thon

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formatting output from a java tool
by vijayalakshmi 15 Jun '13

15 Jun '13

Hi all, I am trying to integrate a tool written in java into galaxy. The tool opens a GUI window to output a graph and also writes a text file. I want to know how to output that graph in the middle pane and how to output the text file so that the user will be able to download it. *Sample.java* public class Sample { public static void main(String[] args) { try { int length = args.length; FileWriter fw = new FileWriter(args[length-1]+".txt"); fw.write("length = " + args.length); for(int i=0;i<args.length;i++) fw.write(args[i]); fw.close(); } catch (Exception e) { e.printStackTrace(); } } } *sample.xml* <tool id="sample" name="Compute correlation"> <description> for the given BAM file </description> <command>java -jar sample.jar $sample_type $window_frame_size $iteration $resolution $correlation_window_size $no_of_CPUs $output</command> <inputs> <param name="sample_type" type="select" label="Choose type of sampling"> <option value="random">Random Sampling</option> <option value="whole">Whole Genome</option> </param> <param name="window_frame_size" type="text" area="true" size="1x10" label="Frame size for extraction" help="Default:50000"/> <param name="iteration" type="text" area="true" size="1x10" label="Number of iterations per chromosome" help="Default:10"/> <param name="resolution" type="text" area="true" size="1x10" label="Resolution" help="Default:1"/> <param name="correlation_window_size" type="text" area="true" size="1x10" label="Correlation window Size" help="Default:1001"/> <param name="no_of_CPUs" type="text" area="true" size="1x5" label="Number of CPUs required" help="Default:1"/> </inputs> <outputs> <data format="txt" name="output" size="1x30" area="true" label="output"/> </outputs> <help> This tool helps plot the correlation function for the given input file </help> </tool> Thanks, VJ.

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Download histories
by Doan, Ryan 14 Jun '13

14 Jun '13

Hello, Several people in our lab would like to download all of their histories from their respective Galaxy accounts. We tried to download them using the following steps: Select "Export to File" Copy the provided link and paste into WGet.exe program as follows: wget.exe --no-check-certificate https://main.g2.bx.psu.edu/history/export_archive?id=e0b0f57abd62f2aa -O F:\Galaxy\Ryan\rnd003bucknell.edu\Cattle_seq.galaxy However, we seem to be getting an error on all files from all of their accounts and no files are being saved. See below for cmd prompt output. Resolving main.g2.bx.psu.edu... 128.118.250.4 Connecting to main.g2.bx.psu.edu|128.118.250.4|:443... connected. WARNING: cannot verify main.g2.bx.psu.edu's certificate, issued by `/C=US/O=Inte rnet2/OU=InCommon/CN=InCommon Server CA': Self-signed certificate encountered. WARNING: certificate common name `bigsky.bx.psu.edu' doesn't match requested hos t name `main.g2.bx.psu.edu'. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/html] Saving to: `C:/Users/RDoan/Documents/Lab_Files/Analysis_Programs/Galaxy/test.txt Is this the correct method to download histories or is there a better solution? Thank you for your help! Ryan

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Tool menu customization :: Card #727
by Björn Grüning 14 Jun '13

14 Jun '13

Hi, thanks to the awesome work from John Chilton in pull request #160 [1] I hacked up a first version of a tool customization that can be controlled by the user [2]. Requested as trello card #727. The user will have a new preference panel (see the attached screenshot) and can toggle several customization options. The options can be specified by each administrator as filter modules under lib/galaxy/tools/filters/. More details in John's original pull request. For example, one use case would be to offer different module sets for different studies. You can specify system-customizations (John's work) with tool_filters = module:function, module:function2 tool_label_filters = ... tool_section_filters = ... and offer user-customizations with: user_tool_filters = examples:restrict_upload_to_admins user_tool_section_filters = examples:restrict_text user_tool_label_filters = ... at the same time. Only user-customizations will be shown in the preference panel. The description of each filter is parsed from the docstring and shown to the user. The patch requires no modification to the database, all user preferences will be stored in user_preference with three special names. Is there any plan from the core development team how such a feature should be addressed. Is that approach flexible enough? It would be great to get some feedback in which direction such a feature should evolve and if its worth to put more time on it. Thanks John, hope you code will be merged! Thanks for your comments, Bjoern [1] https://bitbucket.org/galaxy/galaxy-central/pull-request/160/implement-dyna… [2] https://bitbucket.org/BjoernGruening/galaxy-central-bgruening/commits/68e7b…

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moving galaxy published pages
by Vipin TS 14 Jun '13

14 Jun '13

Hello dev-team, Usually when I want to move a "Galaxy Published Page" between instances I follows these steps: (a) moving workflows and dataset from instance_1 to instance_2 (b) run the workflow at instance_2 (c) create the page at instance_2 So my question is - Can I move/share published pages between instances other than the above way just curious to know, --/Vipin

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galaxy-dev June 2013