galaxy-dev July 2013

galaxy-dev@lists.galaxyproject.org

133 participants
209 discussions

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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Galaxy Local Admin user
by Chadi Abdul Kader El Farran 16 Jul '13

16 Jul '13

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

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provide group(s) association as a tool parameter
by Christian Hundsrucker 16 Jul '13

16 Jul '13

Hi there! Is there an easy way to pass a users group associations to a tool as a parameter. Maybe similar to pass user information via the reserved variable "$__user_email__" ?! I tried "$__app__.model.UserGroupAssociation.group" however I end up with a mapper-object and are kind of stuck here... Thnx, Christian

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Re: [galaxy-dev] Testing with <repeat> parameters
by Joachim Jacob | VIB | 16 Jul '13

16 Jul '13

Oops, I was replying via theGalaxy Development List Archive <http://dev.list.galaxyproject.org/> interface, strange it has put the reply off list... So no functional test for my tool ( despite my enthousiasm :-) ), since the repeat tags must be provided in the test. Thanks, Joachim. Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/16/2013 01:46 PM, Peter Cock wrote: > Off list? > > They don't work yet, bar the simplest case of 0 or 1 repeats using a > single parameter perhaps. > > Peter > > > On Tuesday, July 16, 2013, wrote: > > Hi Peter, > > I was wondering if you have details on how to include tests for > repeat tag sets? > > Cheers, > Joachim > > <quote author='Peter Cock'> > Hello all, > > Should unit tests with repeat parameters work? If so, how do I give > each repeat group in the XML for the <test>? > > Sample tool here: > http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list > > <inputs> > <param name="main_lab" size="30" type="text" value="Venn Diagram" > label="Plot title"/> > <conditional name="universe"> > <param name="type_select" type="select" label="Implicit or > explicit full ID list?"> > <option value="explicit">Explicit</option> > <option value="implicit">Implicit (use union of sets > below)</option> > </param> > <when value="explicit"> > <param name="main" type="data" > format="tabular,fasta,fastq,sff" > label="Full dataset (with all identifiers)" > help="Tabular file (uses column one), FASTA, > FASTQ or SFF file."/> > </when> > <when value="implicit"/> > </conditional> > <repeat name="sets" min="1" max="3" title="Sets"> > <param name="set" type="data" format="tabular,fasta,fastq,sff" > label="Members of set" > help="Tabular file (uses column one), FASTA, > FASTQ or SFF file."/> > <param name="lab" size="30" type="text" value="Group" > label="Caption for set"/> > </repeat> > </inputs> > > The first test attempts to use the repeat "set"/"lab" once - guessing > at how to give repeat parameters in a test: > > <test> > <param name="type_select" value="explicit"/> > <param name="main" value="venn_list.tabular" ftype="tabular"/> > <param name="main_lab" value="Some Proteins"/> > <param name="set" value="rhodopsin_proteins.fasta"/> > <param name="lab" value="Rhodopsins"/> > <output name="PDF" file="venn_list1.pdf" ftype="pdf"/> > </test> > > $ ./run_functional_tests.sh -id venn_list > ... > python /mnt/galaxy/galaxy-central/tools/plotting/venn_list.py > /mnt/galaxy/galaxy-central/database/files/000/dataset_1.dat tabular > "Some Proteins" > /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta > "Rhodopsins" > /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat > fasta "Group" > /mnt/galaxy/galaxy-central/database/files/000/dataset_3.dat > ... > > This seems to have resulted in two <repeat> entries, and so fails. > What I was expecting was: > > python /mnt/galaxy/galaxy-central/tools/plotting/venn_list.py > /mnt/galaxy/galaxy-central/database/files/000/dataset_1.dat tabular > "Some Proteins" > /mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta > "Rhodopsins" > /mnt/galaxy/galaxy-central/database/files/000/dataset_3.dat > > Thanks, > > Peter > ___________________________________________________________ > 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/ > > </quote> > Quoted from: > http://dev.list.galaxyproject.org/Testing-with-repeat-parameters-tp4659840.… > > > _____________________________________ > Sent from http://dev.list.galaxyproject.org >

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Re: [galaxy-dev] Strange behaviour with galaxy history
by Ambrose Andongabo (RRes-Roth) 16 Jul '13

16 Jul '13

Many thanks for the observation. This will come handy next time I hit the same rock. I hope not so soon. Ambrose -----Original Message----- From: Groot, Philip de [mailto:philip.degroot@wur.nl] Sent: 16 July 2013 12:03 To: Carl Eberhard Cc: galaxy-dev(a)lists.bx.psu.edu; Ambrose Andongabo (RRes-Roth) Subject: RE: Strange behaviour with galaxy history Hi Carl, Thank you for your quite extensive answer! I finally managed to find the line in universe_wsgi.ini that caused the problem. The moment I UNCOMMENT the following line: #log_actions = True I no longer can see the histories. The moment I comment this line again everything works fine. Anyway, this exercise resulted in a clean and updated universe_wsgi.ini file and the problem is solved now! Thank you for your help! Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot(a)wur.nl<mailto:Philip.deGroot@wur.nl> Internet: http://www.nutrigenomicsconsortium.nl http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ ________________________________ From: Carl Eberhard [carlfeberhard(a)gmail.com] Sent: 11 July 2013 16:34 To: Groot, Philip de Cc: galaxy-dev(a)lists.bx.psu.edu; Ambrose.Andongabo(a)rothamsted.ac.uk Subject: Re: Strange behaviour with galaxy history Hello, Phillip I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9). Do you see any errors in your log near or after "GET /history/list HTTP/1.1"? Shane Sturrock worked around this problem by updating his universe_wsgi.ini file (if I understand his procedure): 1. Make a backup of your universe_wsgi.ini file (for example, copy it to your home directory) 2. Rename the universe_wsgi.ini file in your galaxy installation something like 'universe_wsgi.ini.saved' 3. Rename the most recent universe_wsgi.ini.sample file (that came with the latest update) to universe_wsgi.ini. 4. Copy any custom settings for your server from your older universe_wsgi.ini.saved file to the newer universe_wsgi.ini file 5. Start Galaxy That seemed to work for Shane. Ambrose re-installed and reconnected his database. Neither is a solution to the original cause, but you may want to try them while we investigate. Thanks, Carl On Thu, Jul 11, 2013 at 5:48 AM, Groot, Philip de <philip.degroot(a)wur.nl<mailto:philip.degroot@wur.nl>> wrote: Hi, First of all, I apologize for interrupting into this discussion, but I have exactly the same problem and did not find a solution yet. And no: prefix and cookies are set properly in our particular setting (as "/")! This is not the cause... I think that the problem occurred with the May Galaxy update, but it was unnoticed for a while. Problem is that the histories of all users are not listed when being asked for it within Galaxy. Only the current history is present for every user. In addition, when I login using another computer, a different history is being depicted (which suggest a cookie issue but I just cannot find it). Copying the current history works but the copy is not listed either. In the postgres database, the histories are properly listed. If I type in the proper history name in Galaxy, I even get the stored history back! So this all works, but users cannot see their histories. The java console does not reveal any problem. prefix and cookie are set properly (I think). So I don't know. Does anyone have any clue on how to tackle this issue? I am happy to provide more information if needed! Thanks! Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786<tel:%2B31-317-485786> F: +31-317-483342<tel:%2B31-317-483342> E-mail: Philip.deGroot(a)wur.nl<mailto:Philip.deGroot@wur.nl><mailto:Philip.deGroot@wur.nl<mailto:Philip.deGroot@wur.nl>> Internet: http://www.nutrigenomicsconsortium.nl<http://www.nutrigenomicsconsortium.nl/> http://humannutrition.wur.nl/ https://madmax.bioinformatics.nl/ -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning. -- This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning.

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galaxy-dev July 2013