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

potential bug in DefaultToolAction collecting chrom info
by Andrew Warren 22 Mar '12

22 Mar '12

Hello, In the file lib/galaxy/tools/actions/__init__.py for the execute function of the DefaultToolAction class line 198 has the following code: if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ): In this case trans.user.preferences[ 'dbkeys' ] is just returning a json string version of the dictionary. The result is that if input_dbkey is a substring of any part of this then it will be returned as True. Something like this would fix (though with the next lines of code it would be converting from json twice): if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string(trans.user.preferences[ 'dbkeys' ] )): Cheers, Andrew

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Clarification on galaxy update process
by Praveen Raj Somarajan 22 Mar '12

22 Mar '12

Hello Dev team, I normally use "hg incoming" to check for any updates and "hg pull -u" to install new updates if available. I noticed that there are files created with ".sample" extension after the update (for all config files) - eg "universe_wsgi.ini.sample" is modified with new updates, but "universe_wsgi.ini" remain unchanged. The recent update has "sanitize_all_html" option integrated, but it added in the "ini.sample" file, not in the original .ini file. I'm quite confused, how does Galaxy pick up this option from .sample? Do I rename .sample to orginal .ini file name to reflect the updates? This is quite difficult as I have made serveral mysql/port/user_dir settings in .ini. Any suggestions would be helpful 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] can the sample tracking system transfer (copy) data to a dataset library not in private Galaxy server data directory tree and then just link files?
by Greg Von Kuster 22 Mar '12

22 Mar '12

Hi leandro, We're resurrecting the Galaxy sample tracking system, so you'll be seeing some work coming from us in this area over the coming weeks. Support for the components will also be more timely and efficient. As usual, contributions are welcome! On Mar 22, 2012, at 8:05 AM, Leandro Hermida wrote: > > Ok just came back to this topic now, realized no this isn't part of > any API, I will have to make code changes somewhere in the lib/galaxy > tree right? > > First, how do I know if I'm using the deferred job runner and transfer > manager method to transfer files from the sequencer? I've set up the > NGS sample tracking system with an external service config to the > sequencer storage area everything really in the standard way you would > set up I would say. What I want to have happen is when the lab people > click to transfer datasets using the sample tracking UI that Set the following in your universe_wsgi.ini file - it's currently not in there, so add it in the section where the other job setting are defined. enable_beta_job_managers = True > > Second, could you tell me where the deferred job plugin code file(s) > are? Then I can make a copy and make the change you mentioned. Look in ~/lib/galaxy/jobs/deferred Greg Von Kuster > > Sorry for needing this help, > Leandro > >

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Restrict tool usage by certain users
by Daniel Sobral 22 Mar '12

22 Mar '12

Hello, At the moment I don't think there is a way to restrict usage of specific tool(s) to specific user(s). Is anyone thinking on developing this kind of functionality? I guess it might be a bit complicated to implement? I guess an "easier" alternative is to have different galaxy instances running, each one with a different tool set? Thanks, Daniel

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Change "Manage data Libraries"
by Sivasangari NANDY 22 Mar '12

22 Mar '12

Hello everyone, I'm trying to change some options in the Manage data Libraries.Especially in the Server Directory, by clicking the "Upload directory of file" in Upload option. So I've changed "universe_wsgi.ini" file and add for library_import_dir my directory. The problem is that I can see only one directory link in Galaxy. I've tried to write two times "library_import_dir" but it's not working, only the last directory is taken into account : library_import_dir = /sequences/fasta/maize/ library_import_dir = /home/***/blastdb_loc/ Also tried to insert a comma but it appears in Galaxy : library_import_dir = /sequences/fasta/maize/, /home/***/blastdb_loc/ Someone has an idea ?Advance thanks, Siva

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version inquiries of galaxy
by springwang＠sjtu.edu.cn 21 Mar '12

21 Mar '12

Dear all, Whether it is ok to any version of some certain software if there is no version number listed in the brackets? For example, liftOver (UCSC) (), Perl (), awk () and etc. Many thanks! Best wishes, Congmao

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quota
by Blanca Andino 21 Mar '12

21 Mar '12

My galaxy account says I am using 184 Gb of space. However, I can only account for 25.5Gb. Best Regards, Blanca

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Can't clone workflows
by Liisa Koski 21 Mar '12

21 Mar '12

Hello, I have lost the ability to clone workflows in my local installation of Galaxy (the latest galaxy-dist). When I try...it just hangs...and hangs... Any help would be much appreciated. Thanks, Liisa

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Re: [galaxy-dev] Looking where to edit web view
by Edward Hills 20 Mar '12

20 Mar '12

Hello Galaxy team, I've recently begun building a resource usage monitor / predictor for Galaxy as part of my Computer Science Honours degree and I was wanting to at some later stage in my project, once the actual resource monitor is built, to incorporate it to the actual Galaxy web interface. have been looking through your code and have found it somewhat difficult to track down where exactly i would go about doing this. I would like to ahve a separate tab up in the top nav bar and then be able to display resource information about Galaxy when its running (processes, I/O, RAM, CPU etc.) Are you able to point me in the right direction for this? Thankyou, Ed

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Re: [galaxy-dev] [galaxy-user] Tophat error
by David Matthews 20 Mar '12

20 Mar '12

Hi Jen, Many thanks for this, much appreciated. Will give it a try - fingers crossed! David. Sent from my phone, so please excuse my mistakes. -----Original Message----- From: Jennifer Jackson Sent: 20/03/2012 18:32 To: David Matthews; Galaxy Dev Cc: galaxy-user; Jeremy Goecks Subject: Re: [galaxy-dev] [galaxy-user] Tophat error Hi David, I don't know if you are still having this problem or not, but I did a web search and found this thread on seqanswers from 2/16 that seems like a good match to the problem you were having: http://seqanswers.com/forums/showthread.php?p=65085 These scientists resolved the problem by removing the "--closure-search" option from the command string. On the Galaxy tool form, this is the option "Use Closure Search:". which is "No" by default. Perhaps you set this to be "Yes"? I would try switching it to "No" to see if that solves the problem. If not, then contacting the tool authors would probably be the best next step, either at seqanswers or directly at tophat.cufflinks(a)gmail.com. The original guess about genome indexes was way off base, this is a python error statement. I don't believe this to be related to the Galaxy wrapper but will cc Jeremy for a second opinion. Hopefully the first option will resolve the issue! Thanks, Jen Galaxy team On 3/14/12 11:10 AM, Jennifer Jackson wrote: > Hi David, > > You question has posted to the list now and we will be getting back to > you. It didn't post immediately due to some mail mailman server issues > here. > > This looks like a problem that came up on a local instance. Because of > that, I am going to send this over to the galaxy-dev(a)bx.psu.edu mailing > list. At first glance, this appears to be a problem with the NGS genome > indexes used for the target genome. These are the instructions you > followed? > http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup (Bowtie indexes are > used for TopHat) > > We will be looking at this more later today, but I wanted to get back to > you, so you that you know that this doesn't need to be posted again. > > Thanks! > > Jen > Galaxy team > > On 3/14/12 6:48 AM, David Matthews wrote: >> Hi, >> >> JUst running a TopHat job which returned the following error: >> >> Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect >> /local/tmp5Ywx45/dataset_942> ./tophat_out/tmp/dataset_942.fa >> [Tue Mar 13 12:45:08 2012] Checking for Bowtie >> Bowtie version: 0.12.7.0 >> [Tue Mar 13 12:45:08 2012] Checking for Samtools >> Samtools Version: 0.1.18 >> [Tue Mar 13 12:45:08 2012] Generating SAM header for >> /local/tmp5Ywx45/dataset_942 >> format: fastq >> quality scale: phred33 (default) >> [Tue Mar 13 12:45:21 2012] Preparing reads >> left reads: min. length=56, count=29523921 >> right reads: min. length=56, count=29543412 >> [Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 >> with Bowtie >> [Tue Mar 13 13:45:26 2012] Processing bowtie hits >> [Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against >> dataset_942 with Bowtie (1/2) >> [Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against >> dataset_942 with Bowtie (2/2) >> [Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against >> dataset_942 with Bowtie >> [Tue Mar 13 15:37:46 2012] Processing bowtie hits >> [Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against >> dataset_942 with Bowtie (1/2) >> [Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against >> dataset_942 with Bowtie (2/2) >> [Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping >> Traceback (most recent call last): >> File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 3063, >> in<module> >> sys.exit(main()) >> File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 3029, in main >> user_supplied_deletions) >> File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 2681, in >> spliced_alignment >> [maps[initial_reads[left_reads]].unspliced_bwt, >> maps[initial_reads[left_reads]].seg_maps[-1]], >> TypeError: list indices must be integers, not str >> >> Does anyone know what this kind of error is? >> >> Best Wishes, >> David. >> >> >> >> __________________________________ >> Dr David A. Matthews >> >> Senior Lecturer in Virology >> Room E49 >> Department of Cellular and Molecular Medicine, >> School of Medical Sciences >> University Walk, >> University of Bristol >> Bristol. >> BS8 1TD >> U.K. >> >> Tel. +44 117 3312058 >> Fax. +44 117 3312091 >> >> D.A.Matthews(a)bristol.ac.uk <mailto:D.A.Matthews@bristol.ac.uk> >> >> >> >> >> >> >> >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ > ___________________________________________________________ > 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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