- galaxy-dev - lists.galaxyproject.org

Fwd: Re: [galaxy-user] Linking to Compressed Data
by Hans-Rudolf Hotz 21 Aug '12

21 Aug '12

moving to dev...... Hi Jen and Brandon well, I don't agree (or maybe I misunderstood the question/answer): we work a lot with compressed data (ie g'zipped fastq files from the sequencer), and link them as a Galaxy data library. We preselect 'fastq' as file format. And then, the first tool in our NGS analysis expects a gzipped fastq file. Regards, Hans -------- Original Message -------- Subject: Re: [galaxy-user] Linking to Compressed Data Date: Mon, 20 Aug 2012 10:32:26 -0700 From: Jennifer Jackson <jen(a)bx.psu.edu> To: Branden Timm <btimm(a)wisc.edu> CC: <galaxy-user(a)lists.bx.psu.edu> Hi Branden, Data in a library needs to be uncompressed in order for Galaxy to index and have access to it correctly. I updated our wiki for the "upload by filesystem link" option: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Good question! Jen Galaxy team On 8/15/12 9:09 AM, Branden Timm wrote: > Hi All, > Is it possible to link to compressed files in a Galaxy data library? > We receive all of our NGS data in bz2 or gzip format for obvious > reasons, just wondering if I have to decompress it on the filesystem > before I link to it or not. Thanks! > > -- > Branden Timm > btimm(a)glbrc.wisc.edu > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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Backup_strategies_for_Galaxy
by Rodolfo Aramayo 21 Aug '12

21 Aug '12

Hi, We are in the process of deploying a small Galaxy server here at Texas A&M University I am a GNU/Linux kind of guy My IT people want to use an SMB-mounted drive share as a backup destination I am concerned that this might impact the performance of the server as in my mind the equation is as follows: SMB=Microsoft=windows=not_GNU/Linux=bad_Idea But then again I am a geneticist Any comments and/or other ideas?? Thanks --Rodolfo

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admin_user not being seen
by Paul-Michael Agapow 21 Aug '12

21 Aug '12

A peculiar quirk - I'm configuring a new Galaxy system for production use and can't get it to recognise my account as an admin, i.e. the admin menu doesn't appear after I've added my email address to the admin_user line in the universe file. Of course, I've restarted the instance multiple times, checked spelling and so forth. It's just not happening. Complication: we're using one Galaxy instance as the webserver with another as a job runner. I don't know if this might cause issues. Okay, any ideas what I might have missed? ------ Paul Agapow (paul-michael.agapow(a)hpa.org.uk<mailto:paul-michael.agapow@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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Rsync error to datacache.g2.bx.psu.edu/indexes
by Joachim Jacob 21 Aug '12

21 Aug '12

Hi all, I'm having issues rsync'ing the reference data of Galaxy $ rsync -avvvzP rsync://datacache.g2.bx.psu.edu/indexes/phiX . opening tcp connection to datacache.g2.bx.psu.edu port 873 rsync: failed to connect to datacache.g2.bx.psu.edu (128.118.201.89): Connection timed out (110) rsync error: error in socket IO (code 10) at clientserver.c(122) [Receiver=3.0.9] [Receiver] _exit_cleanup(code=10, file=clientserver.c, line=122): about to call exit(10) Does anybody has this same issue? Or am I missing something? I have opened my firewall from any port on my laptop to the datacache site port 873 over TCP. Thanks, Joachim -- Joachim Jacob, PhD 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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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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