July 2009 - galaxy-user - lists.galaxyproject.org

by Ido M. Tamir

Hi, a) I have problems with your conception of roles in your RBAC scheme. Normally in RBAC[1] a subject can execute a transaction if the currently active roles of the user allow this. You require that the user should have all of the roles that are currently associated with the library. This makes simple things difficult and complicated things impossible. My policy should be: each user can do everything with his own dataset. the group of a user can access (view and push it to history) the library. a group of bioinformaticians can do everything with allmost all libraries. How would you implement this in your sheme which requires "all of the roles"? Would I have to create a new role for each combination of user/group/bioinformaticians? If you would require just "one of the roles", you would simply add 1) the user as a role to the lib (for everything) 2) the group the user is in as a role to the lib (for pushing to history + view if this is implemented) 3) the bioinformatician group as a role to the lib (for everything) b) An important permission would be to be able to view the item. I played around (maybe not enough) but could not find a way to really hide an item (library, folder, dataset) from the view. c) The little arrow pointing down to bring up the context-menu is very small. It would be helpful if you could maybe make it bigger or turn it into a button. thank you very much, Ido [1] http://csrc.nist.gov/groups/SNS/rbac/documents/Role_Based_Access_Control-...

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August 2009 GMOD Meeting

by Dave Clements, GMOD Help Desk

Hello all, The next GMOD meeting will be held 6-7 August, at the University of Oxford, in Oxford, United Kingdom. Registration is now open. Space is available on a first come, first served basis and there is room for 55 attendees. The meeting cost is £50. See http://gmod.org/wiki/August_2009_GMOD_Meeting to register As with previous GMOD meetings, this meeting will have a mixture of project, component, and user talks. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now (see http://gmod.org/wiki/August_2009_GMOD_Meeting#Agenda_Suggestions). For examples of what happens at a GMOD meeting, see the writeups of the January 2009, July 2008, or any other previous meeting (see http://gmod.org/wiki/Meetings). GMOD meetings are an excellent way to meet other GMOD developers and users and to learn (and affect) what's coming in the project. Please join us in Oxford this August, Dave Clements GMOD Help Desk Note: Unless you have applied to and been admitted to the Summer School, don't you dare register for it. The registration web site will let you do this, but bureaucratic hellishness will ensue. -- * Learn more about GMOD at: ISMB/ECCB: http://www.iscb.org/ismbeccb2009/ (BioMart, Chado, Galaxy, InterMine) * Please keep responses on the list! * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback

12 years, 11 months

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Handling large files in Galaxy

by Brad Chapman

Hi all; I've recently gotten a local Galaxy install up and running for our group. We do a lot of short read sequencing analysis and are looking at Galaxy as a framework to present the data and custom analyses associated with it. One of our main interests is scaling the presentation to large fastq and alignment files. Specifically, we have a case where we'd like to make a large ~300Gb alignment file available to users to query and retrieve sections of alignments corresponding to genomic coordinates. We have a custom C++ program that does this, and would like to plug it in through the tools interface. We'd ideally like to use the Library permissions interface to make this available to certain users. Would anyone be able to offer some advice about the best way to handle this? The standard upload, history, analyze would not be ideal since this large file would be copied around. We've brainstormed 3 different ways to approach this: - Have "special" uploaded files which are actually symlinks to the original file and do not get copied. This looks relatively difficult on my initial assessment. - Pass the logged in user to the C++ program and embed the logic of finding the right file within the external tool. Here we would need some advice about if it were possible to pass the current user through the tools interface. - The hack solution: upload a file that is actually just a link reference to the desired file, and this file gets passed to the external tool. The tool then can read the tiny file, know what large file to access, and proceed from there. This would involve some new datatype integration to handle the hack. I am still relatively uninitiated in the Galaxy way, so could use some advice on if any of these solutions are more likely to work smoothly then others. Generally, what sort of approach is Galaxy taking towards increasingly massive files? Is anyone else doing something similar? Thanks for any thoughts, Brad

12 years, 11 months

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User account weirdness

by Pieter Neerincx

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 ------------------------------------------------------------

12 years, 11 months

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Fresh install has wrong layout

by Chris Cole

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

12 years, 11 months

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how to clear job queue?

by R

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!

12 years, 11 months

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hg17-->hg18 liftover problem

by Stitzel, Michael (NIH/NHGRI) [F]

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

12 years, 12 months

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Roles and access to library items

by Pieter Neerincx

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 ------------------------------------------------------------

12 years, 12 months

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GenomeSpace?

by Erick Antezana

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

12 years, 12 months

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Unnamed histories

by Pieter Neerincx

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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galaxy-user July 2009