- galaxy-user - lists.galaxyproject.org

User account weirdness
by Pieter Neerincx 13 Jul '09

13 Jul '09

Hi, I'm new to Galaxy. It looks pretty impressive, but I'm having a hard time to understand the logic in how user accounts are managed. I created two accounts manually. They are identified using e-mail adresses, but lets refer to them as A and B to keep it short. Then I've setup my galaxy installation to use external authentication with the ldap server of our university. To test whether automatic creation of new accounts works I deleted account A. I also purged the deleted accounts. In the database both accounts are still present. Account A has a 1 in the columns for "deleted" and "purged". Now if I try to login with again the same e-mail address as for A, I would expect a new account will be created, but that is not the case. I can login with account A, but I do not see a new third account popup in the galaxy_user table. Using the admin page from the web interface I can see only one account: B. So somehow the old account is still used although it is no longer visible in the web interface. If I now list the details for account B, I can see that a role with the same name as account A still exists. I can assign this role to B. When I click save and go back to the list of users, the role column for account B is updated from 1 -> 2. I assume this is to indicate that user B now has two roles, although one of them belongs to an account that should not exist. When I go back to the details for account B and remove role A, click save and go back to the overview of users, the column "roles" lists "3" for account B. Going back to the details for B reveals role A was not removed. Trying again won't help to remove role A from user B, but each time I try the amount of roles for user B is incremented with 1 in the overview of users... Therefore I have two questions: Is this the way it is supposed to work? I noticed there are scripts to delete userless histories, purge histories and purge datasets, but how do I really really delete a user? Cheers, Pieter ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Utrecht University Visiting address: H.R. Kruyt building room Z609 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx(a)gmail.com skype: pieter.online ------------------------------------------------------------

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Fresh install has wrong layout
by Chris Cole 13 Jul '09

13 Jul '09

Hi, I've been using the subversion version of Galaxy for a while, but now I want to update to the latest mercurial release. I installed it in a new location as per the wiki and set-up the SGE settings as per my previous install and all the tests pass. It launches fine, but when viewing the website the frames seem to be off-by-one. i.e., the 'Tools' frame is empty except for "This link may not be followed from within Galaxy.", the tools are in the middle window and the 'History' frame has general information. I can't see any errors in the paster.log file, so where can I look to sort out this error? Thanks, Chris

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how to clear job queue?
by R 13 Jul '09

13 Jul '09

I accidentally shut down my galaxy server in the middle of an job execution, after that I try to restart my galaxy server, it always shows the error that a job is in new state, and I can't start my galaxy server at all. I guess I have to clear that job out of the queue, so my galaxy server can start. Does anyone know how to clear the job queue? or any idea how to fix the problem? Thanks a lot!

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hg17-->hg18 liftover problem
by Stitzel, Michael (NIH/NHGRI) [F] 09 Jul '09

09 Jul '09

Hi folks, I am trying to perform a liftover of a UCSC wiggle plot from hg17 coordinates to hg18 coordinates. The file contains chromosome, start position coordinates, end position coordinates, and an intensity column. I didn't see an option to liftover a .wig file in the Galaxy toolbar. Is there a quick workaround or a way to have this implemented in the Galaxy liftover toolbar? Your help is greatly appreciated! Warm Regards, Michael

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Roles and access to library items
by Pieter Neerincx 09 Jul '09

09 Jul '09

Hi, I'm puzzled once more due to the following: * I have an admin account and only one role, which has the same name as my account * Went to the admin page and created a library * Added a file as a dataset to this library * Set permissions so that I am allowed to do anything with both the library as well as with the single item in that library (hence my role is in the various "Roles associated" lists) * When I go to the libraries page, I can see the library, but not the item in it. * If I now move my role for access to the library item to the list of "Roles not associated", click save and go back to the libraries page: * Tada! I can see the library item and add it to my history... works for me, but is rather counter intuitive... Cheers, Pi ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx(a)gmail.com skype: pieter.online ------------------------------------------------------------

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GenomeSpace?
by Erick Antezana 08 Jul '09

08 Jul '09

Hi, I read in http://www.genomeweb.com the following news : "Broad Institute Develops GenomeSpace Platform to Integrate -Omics Tools, Enable Reproducible Workflows June 29, 2009 GenomeSpace will initially integrate six tools — the UCSC Genome Browser, Genomatica, Cytoscape, *Galaxy*, Integrative Genomics Viewer, and GenePattern — but the plan is to eventually enable other developers to easily add their tools to the platform to create a "web 2.0" community for bioinformatics." I was wondering how the Galaxy developers see this integration of Galaxy within such platform? cheers, Erick

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Unnamed histories
by Pieter Neerincx 07 Jul '09

07 Jul '09

Hi, Yet another question: is there a way to control when to get a new unnamed history? Currently I get a new one 9 out of 10 times when I don't need one and when I do need one I can't get one. I'm running galaxy with authentication using a remote ldap server. When I log in I get a new unnamed history, but often I just want to continue where I left the day before. As a result I have all these unnamed histories piling up. At first a deleted them, but then when I needed a new history I could not create one. The only option was to log out and log in again, but the logout button is disabled, because "User controls are disabled when Galaxy is configured for external authentication." Therefore I have to restart my browser loosing the other tabs and windows I had open. So for now I keep a limited supply of spare unnamed histories, but it would be more convenient if galaxy would not automatically create new histories and provide a button to create one if you want one. Cheers, Pi ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Utrecht University Visiting address: H.R. Kruyt building room Z609 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx(a)gmail.com skype: pieter.online ------------------------------------------------------------

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upgrading my local galaxy install
by Erick Antezana 03 Jul '09

03 Jul '09

Hi, I have upgraded my local install by getting the latest source like this: hg pull -u then I compared the *.sample.xml files against my *.xml files (tool_conf.xml). I have also upgraded my DB (from version 6 to 7). I have also launched : sh run_functional_tests.sh and I got a message: ... *** This program requires python version 2.5 or higher *** Current python version is: 2.4.3.final.0 ... I have python 2.4.3. Do I need to upgrade it? During the tests execution I saw the following error messages: ... Test uploading encode data ... ERROR ... ... Gencode Partition ( gencode_partition1 ) > Test-1 ... FAIL ... Stitch MAF blocks ( Interval_Maf_Merged_Fasta2 ) > Test-1 ... FAIL Stitch MAF blocks ( Interval_Maf_Merged_Fasta2 ) > Test-2 ... FAIL ... Summary Statistics ( Summary_Statistics1 ) > Test-1 ... FAIL ... BLAT ( blat_wrapper ) > Test-1 ... FAIL ... Fetch taxonomic representation ( Fetch Taxonomic Ranks ) > Test-1 ... FAIL Poisson two-sample test ( poisson2test ) > Test-1 ... FAIL Poisson two-sample test ( poisson2test ) > Test-2 ... FAIL Compute phastOdds score ( phastOdds_for_intervals ) > Test-1 ... FAIL LAV to BED ( lav_to_bed1 ) > Test-1 ... FAIL ... FAILED (failures=38, errors=5) the rest are OK, some errors and failures I guess are due to the fact that I do not have some tools installed (e.g. BLAT) Do I need to perform any other operation in order to upgrate my local install? (what about the "eggs"? Do I need to check for egg updates? how?) thanks, Erick

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Join EST and Refseq
by Massimo 01 Jul '09

01 Jul '09

Hi, I am trying to join a list of EST generated by UCSC Table (user track) with all bovine Refseq list generated as well from UCSC. The two do not share any common column and I cannot have the EST with the associated Refseq. As suggested by people at UCSC I have generated my list of custom track EST and then I have set the group mRNA and EST track, track mRNA, Table RefSeq gene (reGene) and I have done an intersection with all my ESTs (All refGene records that have any overlap with User Track ). I have then send everything to Galaxy and try to use the join two queries feature but I cannot obtain a unique table with both Refseq and EST accession numbers. I have contacted the people from UCSC but they said that there is a way through Galaxy..but I could not figured it out. Please, let me know if there is a way. Thanks in advance for your help! Massimo Bionaz PhD Post-doctoral researcher Institute for Genomic Biology, University of Illinois 366 Animal Sciences Laboratory 1207 W. Gregory Dr. Urbana, IL 61801 USA Office Tel: 1-217-333-6189 Fax: 1-217-333-8286

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Join EST and Refseq
by Massimo 01 Jul '09

01 Jul '09

Hi, I am trying to join a list of EST generated by UCSC Table (user track) with all bovine Refseq list generated as well from UCSC. The two do not share any common column and I cannot have the EST with the associated Refseq. As suggested by people at UCSC I have generated my list of custom track EST and then I have set the group mRNA and EST track, track mRNA, Table RefSeq gene (reGene) and I have done an intersection with all my ESTs (All refGene records that have any overlap with User Track ). I have then send everything to Galaxy and try to use the join two queries feature but I cannot obtain a unique table with both Refseq and EST accession numbers. I have contacted the people from UCSC but they said that there is a way through Galaxy..but I could not figured it out. Please, let me know if there is a way. Thanks in advance for your help! Massimo Bionaz PhD Post-doctoral researcher Institute for Genomic Biology, University of Illinois 366 Animal Sciences Laboratory 1207 W. Gregory Dr. Urbana, IL 61801 USA Office Tel: 1-217-333-6189 Fax: 1-217-333-8286

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