- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Galaxy Local Admin user
by Hans-Rudolf Hotz 17 Jul '13

17 Jul '13

Please keep all replies on the list by using "reply all" ! for my reply see below... On 07/17/2013 06:58 AM, Chadi Abdul Kader El Farran wrote: > Dear Hans-Rudolf, > > Thank you for your reply. > > The problem was solved by restarting. > > Now my problem is that I am unable to upload files into my Galaxy. > > I have put the following code in Universe_wsgi.ini: > > "# Directories of files contained in the following directory can be uploaded to a library from the Admin view > library_import_dir = /upload" > > However when I upload files to a data library, all files will seem to have no information (0 bytes) > That is very cryptic....and you need to provide more details - did you get an error? - how do you know the files are empty - what happens if you work with the files make sure to follow the wiki page: http://wiki.galaxyproject.org/Admin/DataLibraries/Libraries Hans-Rudolf > Can you kindly help me? > > Thanks a lot for the support. With warmest regards > > > Chadi EL Farran (Post Graduate Student) > Dr. Jonathan Yuin-Han LOH's Laboratory > #08-01, Institute of Molecular and Cell Biology (IMCB) > 61 Biopolis Drive, Proteos > Singapore 138673 > Contact No: +65-91944793 > E-mail: chadi(a)nus.edu.sg > ________________________________________ > From: Hans-Rudolf Hotz [hrh(a)fmi.ch] > Sent: Tuesday, July 16, 2013 9:39 PM > To: Chadi Abdul Kader El Farran > Cc: galaxy-dev(a)bx.psu.edu > Subject: Re: [galaxy-dev] Galaxy Local Admin user > > Hi > > Just double checking: Have you restarted Galaxy? > > > Regards, Hans-Rudolf > > > On 07/16/2013 07:23 AM, Chadi Abdul Kader El Farran wrote: >> Dear Madam/Sir, >> >> I have installed Galaxy Local in our system. I registered as a user. However when I try to give admin status to some users, I am unable despite following the steps mentioned in the help. >> >> >> "To give a user Galaxy admin privileges, add their Galaxy login ( email ) to the list in the following config setting in the Galaxy configuration file universe_wsgi.ini. >> >> # this should be a comma-separated list of valid Galaxy users >> admin_users = user1@bx.psu.edu,user2@bx.psu.edu" >> >> I have done what is mentioned above and the universe_wsgi.ini is edited accordingly. Still when I log on to Galaxy Local I don't see the admin tab. >> >> Can you kindly help me. >> >> With warmest regards >> >> >> Chadi EL Farran (Post Graduate Student) >> Dr. Jonathan Yuin-Han Loh's Laboratory >> #08-01, Institute of Molecular and Cell Biology (IMCB) >> 61 Biopolis Drive, Proteos >> Singapore 138673 >> Contact No: +65-91944793 >> E-mail: chadi(a)nus.edu.sg >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> >

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Postgres renaming to postgresql
by Nikos Sidiropoulos 17 Jul '13

17 Jul '13

Hi all After updating to the last stable galaxy when I'm trying to upgrade the database I'm getting the following message: /steno-internal/projects/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/url.py:105: SADeprecationWarning: The SQLAlchemy PostgreSQL dialect has been renamed from 'postgres' to 'postgresql'. The new URL format is postgresql[+driver]://<user>:<pass>@<host>/<dbname> If I change the line in universe_wsgi.ini from database_connection = postgresql://galaxy:password@localhost:5432/galaxydb to

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repeat tag enhancement?
by Berner, Thomas 17 Jul '13

17 Jul '13

Hey guys, i was searching the mailing list and wiki for some hints if there is a possibility to enhance the repeat tag. We want to give the option to our users to add more than one additional set of the contained parameters at one go e.g. 10 or 20 or 50, because it can be very frustrating to click the "add new dataset" button 50 times. Is there any option to do this with a text field or preset like "add 20 new datasets" or something like that? I would be very thankful for an advice. Greetings, Thomas

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Galaxy-less Tool Installing
by John Chilton 17 Jul '13

17 Jul '13

One of my goals for the GCC was to sell the idea that tool shed repositories need to be installable without a database present. I talked with James Taylor and Enis Afgan about this idea briefly and they seemed to believe this was a good idea - I kept meaning to discuss it with Greg but I never got a good opportunity. Though in past Greg has made this sound potentially doable and has never objected to the goal overtly. I have two specific use cases in mind (CloudBioLinux and LWR), but perhaps the higher-level justification is something along the lines that a lot of effort from Greg and others (Dave, Bjorn, Peter, Nate) has gone into building a modular dependency system that could very easily be leveraged by applications other than Galaxy, so the extra steps that could be taken to make this possible should to make the codebase as broadly useful and to encourage adoption. The Galaxy community could benefit from other applications potentially utilizing and populating the tool shed and Galaxy tool developers would be further incentized to write good, modular dependencies and publish them to the tool shed. A high-level task decomposition would be something like this: 1. Rework installing tool shed repositories to not require a database. A kind of messy way to do this might be adding a use_database flag throughout. A cleaner way might be to use allow the core functionality to work with callbacks or plugins that performed the database interactions. 2. Separate the core functionality out of the Galaxy code base entirely into a reusable, stand-alone library. I would love buy in from the Galaxy team on item 2 above, but it is not strictly needed for my goals - I imagine I could write a script to pull it out Galaxy and build the library automatically or even just have the Galaxy codebase present when using Galaxy-less tool shed dependencies. Buy in on item 1 by the Galaxy team (specifically Greg and Dave B.) however is needed, are there any objections to this idea? Do you have any broad advice on how to approach this to ensure the changes make sense, work with your long term vision, and end up in Galaxy? Of all the things on my TODO list for the next year, this is probably the most potentially broadly interesting to this weeks BOSC codefest attendees, so I was going to attempt to sell this as something to work on. The sales pitch would include building a little tool shed version of the module command - http://linux.die.net/man/1/module to demonstrate this work and have something immediately useful produced. The idea would be to create a command-line tool for utilizing tool shed dependencies. # Unlike standard module, install procedure is available. Probably could # default to main tool shed and latest installable revision % tsmodule repo:install galaxyp/tint % tsmodule repo:install toolshed.g2.bx.psu.edu/galaxyp/tint/ab43b5ba7a4e # module lets you list packages, I guess tool shed version would need # repository and package listings: % tsmodule repo:list toolshed.g2.bx.psu.edu/galaxyp/tint/ab43b5ba7a4e % tsmodule package:list tint_proteomics_scripts/1.19.19/galaxyp/tint/ab43b5ba7a4e # Finally, a use command would source the env.sh script and make dependency # available in the command-line (might require starting new shell?): % tsmodule package:use tint_proteomics_scripts % tsmodule package:use tint_proteomics_scripts/1.19.19 % tsmodule package:use int_proteomics_scripts/1.19.19/galaxyp/tint/ab43b5ba7a4e # use apps that would be available to tools with valid requirements tags. % iQuantCLI This would be different from using the API scripts because there would be no API, Galaxy instance, or Galaxy database involved - just the Galaxy code. If this was able to split into its own Python library, one could imagine even allowing something like tsmodule to be installable right from pip and recursively fetch a toolshed_client library or something like that.

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Visualization in galaxy
by sridhar srinivasan 16 Jul '13

16 Jul '13

Dear Developers, I could see the visualize icon in the History page below the output file.. Actually i am trying to plot the graph between the column 4 and 8 from the output.. I tried using the visualize option, But takes long time to and i could'nt get the plot.. Please suggest , how to get the Scatter plot your suggestions are very much appericiated.. Thanks Sridhar

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toolshed repository down?
by Linda Cham 16 Jul '13

16 Jul '13

Hi. Getting error when trying to install the latest Galaxy on a new stand alone linux RH server. Is the repository down? migrate.versioning.repository DEBUG 2013-07-16 14:14:46,235 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_tools', 'repository_id': ' GalaxyTools'}} tool_shed.galaxy_install.migrate.check DEBUG 2013-07-16 14:14:46,240 psycopg2 egg successfully loaded for postgres dialect The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_… raised the exception: <urlopen error [Errno 110] Connection timed out> The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=bowtie_… raised the exception: <urlopen error [Errno 110] Connection timed out> The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz&o… raised the exception: <urlopen error [Errno 110] Connection timed out> The URL http://toolshed.g2.bx.psu.edu/repository/get_tool_dependencies?name=lastz_p… raised the exception: <urlopen error [Errno 110] Connection timed out> Traceback (most recent call last): ....... return tool_shed_accessible, missing_tool_configs_dict UnboundLocalError: local variable 'missing_tool_configs_dict' referenced before assignment Regards, Linda

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Potential Bug when installing Tool dependencies
by Michael E. Cotterell 16 Jul '13

16 Jul '13

There's a bug in central and dist where a virtual environment defined as a tool dependency will fail to install packages via pip if the absolute path to the virtual environment `venv_directory` contains any spaces (i.e., a directory with a space in it exists on that path). I was able to fix the problem and have issued a pull request, but it looks like no one has looked at it yet: https://bitbucket.org/galaxy/galaxy-central/pull-request/195/allow-pip-to-r… Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Faculty Liaison, CS Graduate Student Association, University of Georgia mepcotterell(a)gmail.com (mailto:mepcotterell@gmail.com) mepcott(a)uga.edu (mailto:mepcott@uga.edu) mec(a)cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/

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CloudMan Error
by greg 16 Jul '13

16 Jul '13

Hi guys, I'm hitting an error using CloudMan using the Share-an-Instance option. It says: Error creating volume from shared cluster's snapshot '['snap-cfa775ba']': 'filesystems'. Also disk stats says 0 /0 and the Applications light is yellow while the data light is green. I'm using the share string cm-808d863548acae7c2328c39a90f52e29/shared/2012-09-17--19-47 It's always worked in the past. Thanks, Greg Here's the full log: 14:58:18 - Master starting 14:58:20 - Completed the initial cluster startup process. This is a new cluster; waiting to configure the type. 14:58:24 - Migration service prerequisites OK; starting the service 14:58:24 - SGE service prerequisites OK; starting the service 14:58:31 - Setting up SGE... 14:58:51 - HTCondor service prerequisites OK; starting the service 14:58:51 - HTCondor config file /etc/condor/condor_config not found! 14:58:59 - Hadoop service prerequisites OK; starting the service 14:59:48 - Done adding Hadoop service; service running. 15:01:45 - Error creating volume from shared cluster's snapshot '['snap-cfa775ba']': 'filesystems'

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DRMAA Runner URL Specify TORQUE host
by Bart Gottschalk 16 Jul '13

16 Jul '13

Is it possible to specify the torque host as part of a DRMAA runner URL? I haven't been able to find a *native_options *parameter to allow for this. I'm using the old style cluster configuration. *drmaa://[native_options]/* * * Also, I haven't been able to find a list of native_options anywhere. Does such a list exist? If so, where?

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Re: [galaxy-dev] To move galaxy local Production Instance to a new server setup
by Madhuri Kota 16 Jul '13

16 Jul '13

Dear All, We have had a working local galaxy instance being used with mySQL for almost two years with a lot of new scripts, workflows built-in and datasets still associated with it. We now would like to move to a new server but rather than start from scratch, would like to move all parts of current instance as is first. We ran deploy_galaxy.sh of galaxy-admin-utils-master, modifying "hg clone to point to our current instance". As it copied the virtual environment details also, I expected to be able to run start_galaxy.sh without requiring new eggs to be compiled. Where did I go wrong. Is it always required to re-compile them? Or is there a way to copy the missing eggs. Please advise. Error last few lines: Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 37, in <module> c.resolve() # Only fetch eggs required by the config File "/home/ocimum/GalaxyMigrated/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/home/ocimum/GalaxyMigrated/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/home/ocimum/GalaxyMigrated/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/home/ocimum/GalaxyMigrated/galaxy_venv/local/lib/python2.7/site-packages/distribute-0.6.24-py2.7.egg/pkg_resources.py", line 584, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. Regards, Madhuri ________________________________ 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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