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

Loc file configuration question
by Raja Kelkar 10 May '12

10 May '12

I have two questions that pertain to a local install of galaxy: 1. I have been having trouble getting the “fetch sequences” à “extract genomic DNA” tool to work. Can someone identify the specific *.loc file that needs to have the info about the location of the genome sequence files? I get the following error when I run the extract tool: *No sequences are available for 'hg19’, request them by reporting this error.* * * 2. What configuration file(s) need to contain locations for the gtf/gff files? Thanks.

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Error when exporting history to file
by Sarah Diehl 10 May '12

10 May '12

Hi all, I get the following error when I try to export a specific history to file: 10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive HTTP/1.1" 500 - "http://galaxy.immunbio.mpg.de/" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/20111108 Fedora/3.6.24-1.fc14 Firefox/3.6.24" Error - <type 'exceptions.TypeError'>: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file... Any help is greatly appreciated! Best regards, Sarah

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Running Galaxy on PBS/Torque cluster
by Dorset, Daniel C 10 May '12

10 May '12

I have had Galaxy running on a local BAS, and after success with that we're ready to create an instance on our local cluster computing service. The local cluster uses PBS/Torque. I'm familiar with the basics of configuration, but our particular scheduler rewards those who specify accurate walltimes. I would like to be able to define specific walltimes for each tool. I'm mapping out a strategy for how best to specify accurate walltimes. For instance, if someone is running tophat, it will take longer if they're mapping against a complex reference genome like human, as opposed to nematode. I'd like to use different walltimes to account for that. Is there anyone who has tackled this and would be willing to share their approach with me? Thanks! Dan

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Installing Galaxy on Mac OS X 10.7: pyglet issue
by Arnav Moudgil 10 May '12

10 May '12

Hi folks, I'm trying to install Galaxy locally on my Mac running OS X 10.7 and Python 2.7.3. After cloning the repository and running sh run.sh the first time, the following error occurs: [Fetches series of eggs…] Fetch successful. Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/Users/username/Downloads/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 73, in run commands = get_commands() File "/Users/username/Downloads/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 115, in get_commands plugins = pluginlib.resolve_plugins(plugins) File "/Users/username/Downloads/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/pluginlib.py", line 81, in resolve_plugins pkg_resources.require(plugin) File "/Users/username/Downloads/galaxy-dist/lib/galaxy/eggs/__init__.py", line 413, in require return pkg_resources.working_set.require( req_str ) File "/Users/username/Downloads/galaxy-dist/lib/pkg_resources.py", line 666, in require needed = self.resolve(parse_requirements(requirements)) File "/Users/username/Downloads/galaxy-dist/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: Not Found: pyglet-1.1.4-py2.6 (did you run python setup.py develop?) I have downloaded and installed pyglet for both Python 2.7 and 2.6 (both versions are on my system, but 2.7 is default), and the error still persists. Any ideas what's going on here? Thanks!

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Submitting Jobs as User
by Daniel Patrick Sullivan 10 May '12

10 May '12

Hi, Galaxy Developers, I have a hopefully quick question regarding configuring Galaxy cluster integration; I've configured our universe_wsgi.ini to include the options specified in this document: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_… set_metadata_externally = True set_metadata_externally = True drmaa_external_runjob_script = scripts/drmaa_external_runner.py drmaa_external_killjob_script = scripts/drmaa_external_killer.py I have also given the galaxy account full sudo privileges. My question is that even after re-starting Galaxy and launching a job, when I schedule a job through galaxy, the job is still being scheduled as the galaxy user (if I run qstat, for example). Could anybody possibly provide some insight as to why this would be occurring? Do I need to set any other configuration options other than what I have specified above? Thank-you so much, Dan Sullivan

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Re: [galaxy-dev] [galaxy-user] Help on installing cutadapt
by Tilahun Abebe 10 May '12

10 May '12

Hi Jen, Thank you for the suggestions. I did try to log in to Galaxy under User -->Login. The password is the one I use for the Galaxy Main. However, it gives me the error message "No such user (please note that login is case sensitive)". I do not see a place to set Admin password in the universe_wsgi.ini file. Here is how I setup the Admin permissions under Users and Security in the universe_wsgi.ini file: 1. id_secrete = gave a mix of numbers and letters 2. use_remote_user = True 3. remote_user_maildomain = Tilahun.Abebe(a)uni.edu 4. remote_user_logout_href = None 5. Admin_users = Tilahun.Abebe(a)uni.edu 6. require_login = True 7. allow_user_creation = False 8. allow_user_deletion = True 9. allow_user_impersonation = True 10. allow_user_dataset_purge = True 11. new_user_dataset_access_role_default_private = True Can you check and let me know information I missed? Thanks. Tilahun ------------------ On Tue, May 8, 2012 at 4:53 PM, Jennifer Jackson <jen(a)bx.psu.edu> wrote: > Hello Tilahun, > > Are you logged into your Galaxy instance UI using your admin account? This > will display the Admin menu. > > Admin permissions are set up in the universe_wsgi.ini file: > > # -- Users and Security > > < other items > > > # Administrative users - set this to a comma-separated list of valid Galaxy > # users (email addresses). These users will have access to the Admin > section > # of the server, and will have access to create users, groups, roles, > # libraries, and more. For more information, see: > # http://wiki.g2.bx.psu.edu/**Admin/Interface<http://wiki.g2.bx.psu.edu/Admin/Interface> > #admin_users = None > > Hopefully this solves the issue. Going forward, you'll probably find that > the galaxy-dev(a)bx.psu.edu mailing list is the most helpful for local > install questions: > http://wiki.g2.bx.psu.edu/**Support#Mailing_Lists<http://wiki.g2.bx.psu.edu/Support#Mailing_Lists> > > Best, > > Jen > Galaxy team > > > On 5/8/12 2:10 PM, Tilahun Abebe wrote: > >> Hi Galaxy users, >> >> I tried to install cutadapt for sequence trimming on a local Galaxy >> instance. I successfully installed Galaxy as an administrator. However, >> when Galaxy starts, I don't see the administrator option in the top menu >> bar with the "Analyze Data, Workflow, Shared Data, Visualization, Help, >> and User". It looks like the only way I can install cutadapt is with an >> administrator option. Any suggestion how I can include the administrator >> option in the menu? >> >> Thanks for your help. >> >> Tilahun >> >> >> >> ______________________________**_____________________________ >> 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<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 >

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Server Error when downloading files from history
by Rathi D. Thiagarajan 10 May '12

10 May '12

Hi there, I received the following error when trying to download/save my tabular files with 5k lines: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Please help! Thanks in advance. Cheers, Rathi -- Rathi D. Thiagarajan, PhD Professional Scientific Collaborator UCSD Research Scholar Dept. of Chemical Physiology Center for Regenerative Medicine The Scripps Research Institute 3030 Science Park Rd, La Jolla, CA 92035, USA Mail:SP30-3021 W: 858.784.7753 E: rathi(a)scripps.edu E: rthiagarajan(a)ucsd.edu

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Trackster - not showing data.
by Mohammad Heydarian 10 May '12

10 May '12

Hi, I have been trying to use trackster on the main Galaxy server for a couple of days now. It was working fine for me early yesterday, I was looking at (larger) BAM files, then it just stopped and would not display the data of the loaded tracks (but did display the track title). I have tried to start Trackster with smaller sized tracks, as well as using another Galaxy account, and still cannot get Trackster to display data (though it will show the track title). Any help would be greatly appreciated! Cheers, Mo Heydarian

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debugging jobs in 'new' state
by Shantanu Pavgi 10 May '12

10 May '12

We experienced an issue where some of the galaxy jobs were sitting in the 'new' state for a quite long time. They were not waiting for cluster resources to become available, but haven't been even queued up through DRMAA. We are currently using non-debug mode and following were my observations: * No indication of new jobs in paster.log file * database/pbs script didn't contain any associated job scripts * in backend database - job table contained their galaxy job id but no command_line input was recorded Also, not all the jobs are waiting in the 'new' state. Many jobs submitted after above waiting jobs got completed successfully on the cluster. Is there any job submission logic within galaxy which is being used for submitting jobs? Any clues on how to debug this issue will be really helpful. -- Thanks, Shantanu.

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permission error
by Alex Strunnikov 09 May '12

09 May '12

Hello, I am trying to use MACS on galaxy at https://main.g2.bx.psu.edu/, but I get permission error: Error executing tool: [Errno 13] Permission denied: '/galaxy/main_pool/pool3/files/004' Could you help, please Sincerely, alex strunnikov my login is alex(a)gibh.org

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