August 2012 - galaxy-dev - lists.galaxyproject.org

dynamic update of tool data files
by Marc Logghe 21 Aug '12

21 Aug '12

Hi all, I am wondering what is the best way to dynamically update tool data files without having to restart Galaxy. The context is as follows. A cron job is regularly creating new blast databases (or in general: e.g. tool data needed to fill a dropdown list). The same cron job could be adapted so that the corresponding galaxy tool data file is updated as well. But I don't think it is possible to make Galaxy aware of the new data without restarting, is it ? Or should one follow the root of shared library datasets ? But then, how to configure a tool so that this dataset is used (without manual import into a history ?) Thanks, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________

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cuffdiff output
by suzan katie 20 Aug '12

20 Aug '12

Hello, I am new to using Galaxy tools. I am running paired end RNA-Seq data on Galaxy and I want to differential gene expression between control and treated samples I was fine until running TopHat output, I am having problems with cufflinks and cuffdiff output. I ran the cufflinks and cuffdiff twice, once with reference annotation and once without reference annotation (Imported form UCSC). Output with reference annotation produced output with gene ids naming usc## Output without reference annotation produced output with gene ids naming CUFF1.### Can anyone suggest how to get gene names instead of just numbers? Thanks suz

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Trackster Bug
by SHAUN WEBB 20 Aug '12

20 Aug '12

Hi, not sure if this has been reported yet. If I use the dataset icon to view in trackster then select view in saved visualisation, the saved visualisations pop up momentarily then the window closes. I've tested this on the main galaxy site and my own instance on Chrome and Firefox. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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grouping/separating parameters on the page
by Dan Tenenbaum 20 Aug '12

20 Aug '12

Hello, Is there a way to do one or both of the following: 1) Group a set of related parameters together on a tool page 2) Put a separator in between related groups. I have a tool with lots of parameters. It's ok to have them all on one page but I'd like to have some space or a line between the related groups (and maybe even a header for the group) so that users know which parameters are related. Thanks, Dan

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Galaxy Reports no longer functions
by Iry Witham 20 Aug '12

20 Aug '12

Hi Team, Since I upgraded to the latest galaxy-dist I can no longer get the reports interface to function. When I go to galaxy:9001 I get the following server error: An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). The reports_webapp.log is as follows: python path is: /hpcdata/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip, /usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages/Numeric, /usr/lib64/python2.6/site-packages/gtk-2.0, /usr/local/lib64/python2.6/site-packages galaxy.model.custom_types DEBUG 2012-08-07 17:13:53,219 psycopg2 egg successfully loaded for postgres dialect galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,792 Enabling 'users' controller, class: Users galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,815 Enabling 'system' controller, class: System galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,909 Enabling 'sample_tracking' controller, class: SampleTracking galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,922 Enabling 'jobs' controller, class: Jobs galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,942 Enabling 'workflows' controller, class: Workflows galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,947 Enabling 'root' controller, class: Report galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,950 Enabling 'httpexceptions' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,971 Enabling 'recursive' middleware /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/serial_number_generator.py:11: DeprecationWarning: the md5 module is deprecated; use hashlib instead import md5 galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,708 Enabling 'error' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,749 Enabling 'trans logger' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,750 Enabling 'config' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,888 Enabling 'x-forwarded-host' middleware Starting server in PID 6345. Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 303, in command serve() File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 287, in serve server(app) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 151, in server_wrapper **context.local_conf) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1314, in server_runner serve(wsgi_app, **kwargs) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1264, in serve threadpool_options=threadpool_options) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1114, in __init__ RequestHandlerClass, ssl_context) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1094, in __init__ RequestHandlerClass, ssl_context) File "/hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 328, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib64/python2.6/SocketServer.py", line 400, in __init__ self.server_bind() File "/usr/lib64/python2.6/BaseHTTPServer.py", line 108, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib64/python2.6/SocketServer.py", line 411, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: [Errno 98] Address already in use Removing PID file reports_webapp.pid The following is the report_wsgi.ini: # ---- HTTP Server ---------------------------------------------------------- [server:main] use = egg:Paste#http port = 9001 host = 127.0.0.1 use_threadpool = true threadpool_workers = 10 # ---- Galaxy Webapps Report Interface ------------------------------------------------- [app:main] # Specifies the factory for the universe WSGI application paste.app_factory = galaxy.webapps.reports.buildapp:app_factory log_level = DEBUG # Database connection #database_file = database/universe.sqlite # You may use a SQLAlchemy connection string to specify an external database instead # database_connection = postgres:///galaxy_test?user=postgres&password=postgres database_connection = postgres:///galaxy_1?user=galaxy&password=galaxy # Where dataset files are saved file_path = database/files # Temporary storage for additional datasets, this should be shared through the cluster new_file_path = database/tmp # Session support (beaker) use_beaker_session = True session_type = memory session_data_dir = %(here)s/database/beaker_sessions session_key = galaxysessions session_secret = changethisinproduction # Configuration for debugging middleware # debug = true use_lint = false # NEVER enable this on a public site (even test or QA) # use_interactive = true # path to sendmail #sendmail_path = /usr/sbin/sendmail # Address to join mailing list #mailing_join_addr = galaxy-user-join(a)bx.psu.edu # Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) ## use_heartbeat = True # Profiling middleware (cProfile based) ## use_profile = True # Mail smtp_server = smtp.jax.org error_email_to = cbr-help(a)jax.org # Use the new iframe / javascript based layout use_new_layout = true # Serving static files (needed if running standalone) static_enabled = True static_cache_time = 360 static_dir = %(here)s/static/ static_images_dir = %(here)s/static/images static_favicon_dir = %(here)s/static/favicon.ico static_scripts_dir = %(here)s/static/scripts/ static_style_dir = %(here)s/static/june_2007_style/blue I am sure I have something misconfigured, but can't seem to figure it out. Thanks for the assistance. Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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Question about default input files
by Huayan Gao 19 Aug '12

19 Aug '12

Dear Nate, I am writing a tool of my own. I have a question about the default input files. I'd like to include some test files for my tool so anyone who is using the tool can run the tool with my default files or the files they upload. How can I set it up or where should I put the default input files? Thanks, Huayan

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(no subject)
by ashwinikumar＠utdallas.edu 19 Aug '12

19 Aug '12

MY Y Sent from my iPhone

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pipeline execution succeeds but galaxy shows failure
by Brian Haas 17 Aug '12

17 Aug '12

Hi, I wrote a pipeline (xml attached) that, from what I can gather, succeeds, but galaxy shows it as an error and doesn't make the output file accessible as a new data set. >From the server log, I can see that the command line is being constructed correctly, and it even indicates that it's captured the output, but in the display of the web browser, it just shows up in the error state. The script being run exits (0) on success. Any ideas? Here's what the output section of my xml file looks like: <outputs> <data format="bam" name="coordSortedBam" label="${tool.name} on ${on_string}: coord-sorted read alignments" from_work_dir="alignment/alignment.coordSorted.bam"/> </outputs> and here's what the server log states: galaxy.jobs.handler INFO 2012-07-20 09:52:05,240 (30) Job dispatched galaxy.jobs.runners.local DEBUG 2012-07-20 09:52:05,453 executing: alignReads.pl --target /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_26.dat -o alignment --aligner bowtie --single /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_23.dat --seqType fq galaxy.jobs DEBUG 2012-07-20 09:52:16,673 finish(): Moved /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/job_working_directory/000/30/alignment/alignment.coordSorted.bam to /Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_50.dat as directed by from_work_dir Again, as far as I can tell, everything worked - but the browser doesn't think so. I've run the exact command above on the command-line, and it exits(0) indicating success. Also, I've verified that when run through my galaxy instance, the galaxy-relocated output file is as expected. Many thanks for your help. I'm still getting my feet wet with galaxy, reading through all the documentation and searching the mailing list for additional help. best regards, -brian -- -- Brian J. Haas Manager, Genome Annotation and Analysis, Research and Development The Broad Institute http://broad.mit.edu/~bhaas

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TopHat Wrapper to handle Multiple Fastq reads
by Vijaykant N 17 Aug '12

17 Aug '12

Greetings, I was working on the TopHat wrapper (we have customized one for handling just one input Fastq read) for handling multiple reads. I figured out that using repeat tag was the way forward, but have been having a hard time with the Cheetah template. Any help or suggestions? Sincerely, Vijay

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optional="false" not working?
by Dan Tenenbaum 17 Aug '12

17 Aug '12

Hello, I have the following wrapper: <tool id="foo" name="foo" version="0.99.0"> <description>foo</description> <command interpreter="python"> tool.py $outputFileName </command> <inputs> <param name="tp" type="text" label="label" help="help" optional="false"/> </inputs> <outputs> <data format="csv" name="outputFileName"/> </outputs> </tool> I expect that when I click "Execute" I will be told that "tp" must have a value. However, that doesn't happen, it just goes ahead and executes the script. How do I get Galaxy to require that a text param have a value? Thanks, Dan

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