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

Follow up on GATK v2.x thread
by Geraldine Van der Auwera 17 Sep '12

17 Sep '12

Hi Galaxy-dev, A small point of clarification to follow up on this exchange: http://gmod.827538.n3.nabble.com/GATK-v2-x-td4024851.html In this exchange, JT mentions "those [tools] which remain under the open source license (basically, GATK 1.6)". I assume he means GATK Lite, which includes the core GATK architecture, engine and all tools that were present in v1.6, all of which indeed remain completely open-source under the new license. What I would like to clarify is that while GATK Lite is the continuation of the 1.6 development branch, it is more appropriately referred to as version number "2.x (lite)". I realize there may be some confusion about the version numbering and what exactly is or isn't open-source now, so if you have any questions please feel free to email me directly at vdauwera(a)broadinstitute.org or post your question in our support forum at http://gatkforums.broadinstitute.org/ Regards, Geraldine

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Remote authentication in Toolshed / Community_wsgi.ini syntax
by Jean-Christophe Ducom 17 Sep '12

17 Sep '12

All- I'm trying to get the external user authentication (LDAP) to work with our local toolshed installation. I replicated the exact implementation that works with our local Galaxy installation The following lines use_remote_user = True remote_user_maildomain = scripps.edu were added in community_wsgi.ini When I try to authenticate I get the following error message: ---------- URL: https://toolshed.scripps.edu/ File '/gpfs/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/gpfs/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/gpfs/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/gpfs/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/gpfs/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/gpfs/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 134 in __call__ trans = self.transaction_factory( environ ) File '/gpfs/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 187 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/gpfs/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 207 in transaction_chooser return GalaxyWebUITransaction( environ, galaxy_app, self, session_cookie ) File '/gpfs/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 870 in __init__ self._ensure_valid_session( session_cookie ) File '/gpfs/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 372 in _ensure_valid_session user_for_new_session = self.get_or_create_remote_user( remote_user_email ) File '/gpfs/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 480 in get_or_create_remote_user if not user.default_permissions: AttributeError: 'User' object has no attribute 'default_permissions' ------- It looks like other directives that work in universe_wsgi.ini such as (allow_user_deletion = True) do not work in community_wsgi.ini Am I missing something? Is there any special to do for external authentication for local toolshed installation? How can users be deleted from toolshed database from the toolshed Admin tools? Thank you for any insight JC

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A Galaxy environment that can support up to 35 users?
by Dan Sullivan 17 Sep '12

17 Sep '12

Hi, Galaxy Developers, Is anybody out there managing a Galaxy environment that was designed and or has been tested to support 35 concurrent users? The reason why I am asking this is because we [the U of C] have a training session coming up this Thursday, and the environment we have deployed needs to support this number of users. We have put the server under as high as stress as possible with 6 users, and Galaxy has performed fine, however it has proven somewhat challenging to do load testing for all 35 concurrent users prior to the workshop. I can't help but feel we are rolling the dice a little bit as we've never put the server under anything close to this load level, so I figured I would try to dot my i's by sending an email to this list. Here are the configuration changes that are currently implemented (in terms of trying to performance tune and web scale our galaxy server): 1) Enabled proxy load balancing with six web front-ends (the number six pulled from Galaxy wiki) (Apache): <Proxy balancer://galaxy/> BalancerMember http://127.0.0.1:8080 BalancerMember http://127.0.0.1:8081 BalancerMember http://127.0.0.1:8082 BalancerMember http://127.0.0.1:8083 BalancerMember http://127.0.0.1:8084 BalancerMember http://127.0.0.1:8085 </Proxy> 2) Rewrite static URLs for static content (Apache): RewriteRule ^/static/style/(.*) /group/galaxy/galaxy-dist/static/uchicago_cri_august_2012_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /group/galaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /group/galaxy/galaxy-dist/static/$1 [L] RewriteRule ^/robots.txt /group/galaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) balancer://galaxy$1 [P] 3) Enabled compression and caching (Apache): <Location "/"> SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary </Location> <Location "/static"> ExpiresActive On ExpiresDefault "access plus 6 hours" </Location> 4) Configured web scaling (universe_wsgi.ini) : a) six web server processes (threadpool_workers = 7) b) a single job manager (threadpool_workers = 5) c) two job handlers (threadpool_workers = 5) 5) Configured a pbs_mom external job runner (our cluster), and commented out the default tool runners (to use pbs) (we are not using the other tools for the workshop). #ucsc_table_direct1 = local:/// #ucsc_table_direct_archaea1 = local:/// #ucsc_table_direct_test1 = local:/// #upload1 = local:/// 6) Changed the following database parameters (universe_wsgi.ini): database_engine_option_pool_size = 10 database_engine_option_max_overflow = 20 7) Disable the developer settings (universe_wsgi.ini): debug = False use_interactive = False #filter-with = gzip The server I have is a VM with the following resources: 2GB of RAM 4CPU Cores I feel that it is also worthwhile to mention that users will not be downloading datasets during the workshop, so as of now, the implementation of "XSendFile" as specified in the Apache Proxy documentation is not of immediate concern. Does anybody see any blaring mistakes where they think this configuration might fall short with respect to capacity planning for an environment of 35 concurrent users, or additional tuning that could potentially assist in ensuring the availability of the server during the workshop? Thank-you so much for your opinion(s), and please wish us luck this Thursday :-) Dan Sullivan

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Choosing between pre-existing file or user-defined file as tool input
by Makis Ladoukakis 17 Sep '12

17 Sep '12

Hello, I am building a new tool for Galaxy and I would like for it to have an option for the user to choose his file for input or to use a pre-installed file on the server (in a specific path not defined by the user). Can anyone tell me which is the right parameter type to use in the configuration file? Thank you in advance, Makis Ladoukakis

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The Tools API
by Ahmet Yildiz 17 Sep '12

17 Sep '12

Hi, When will be the tools API completely available, is there any concrete plans for that. I can't load any tool information with repeat and conditional inputs. Best regards Ahmet

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Why doesn't bowtie in galaxy accepting colorspace reads directly?
by Praveen Raj Somarajan 17 Sep '12

17 Sep '12

Hi All, I'm wondering why the Bowtie version in (even latest) Galaxy does NOT support .csfasta/.qual input files directly, though it is mentioned under "Map with Bowtie for SOLiD". This is the case of "BWA for SOLiD" as well. One would expect direct support on colorspace files. Do you have any plans of implementing this?I see this would be a great support to SOLiD users. Look forward to your comments Thanks, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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Re: [galaxy-dev] Workflow Queue
by Hans-Rudolf Hotz 17 Sep '12

17 Sep '12

Please keep all replies on the list by using "reply all" - this way, others might be able to jump in and provide further help. Regards, Hans On 09/16/2012 09:25 AM, Edward Hills wrote: > Hi Hans, > > Thanks for that however I need to do this programmatically without > access to the UI. I am building a resource monitor / predictor for > Galaxy and so need to know all the tools in the workflow before it > executes and only from the command line. > > Thanks, > Ed > > On Thu, Sep 13, 2012 at 6:59 PM, Hans-Rudolf Hotz <hrh(a)fmi.ch > <mailto:hrh@fmi.ch>> wrote: > > Hi Edward > > Select 'view' instead of 'run' in your workflow list. This will give > you a nice (human readable) overview of all the steps, or select the > download option to get an xml describing your workflow. > > Regards, Hans > > > > > On 09/13/2012 03:20 AM, Edward Hills wrote: > > Hi Galaxy team, > > I am wanting to know where to find the queue that stores all > tool's that > are going to be executed in the pipeline. > > For example, I am running a workflow of 5 tools all linked > together (the > details are not important). Programatically I wish to know the > names of > the tools that are going to be run. > > This is because I wish to perform some pre-run analysis on all > the tools > in the workflow before they get executed. > > Thanks, > Edward Hills > > Department of Biochemistry, > University of Otago, > Dunedin, > New Zealand. > > > _____________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > >

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Return Files
by Alfredo Guilherme Silva Souza 16 Sep '12

16 Sep '12

Good Afternoon! I need a help. I am developing a tool in the galaxy, but I have a process that runs in the background, so that it terminates an email is sent to the user informing the end of the run, I could send the data via email, the more I need to return the data in a archive. zip to the galaxy, however only if you are not running in the background. A nice idea would be so user login or update your list of jobs I return to him the result of the execution of my tool. Hugs. -- *Alfredo Guilherme* * *

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reinstall
by Paul Tanger 14 Sep '12

14 Sep '12

So I successfully added the emboss tools to galaxy, but I failed to create a tool panel section for them. So I thought I would uninstall them and install them again, this time creating a tool panel section. I'm following the instructions here ( http://wiki.g2.bx.psu.edu/Tool%20Shed#Deactivating_and_uninstalling_tool_sh… ), but I'm getting this error when trying to reinstall the tool repository: AttributeError: 'NoneType' object has no attribute 'endswith' Any ideas what I should do to get this reinstalled? Thanks!

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Error with Heatmap : need bx-python while it's installed
by julie dubois 14 Sep '12

14 Sep '12

Hi all, I have a problem with one of applications of galaxy-cistrome : when I run the application Heatmap, it didn't work and the log says me : "need bx-python" It's very clear. but on another pc with same installation, Heatmap run and furthermore bx-python is installed with your procedure : in galaxy-env mode with easy_install bx-python and no error message appear during this installation. Any idea of where can the problem come ? Thanks. julie

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