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

Problem inGetting user name
by sshashi 24 Jun '12

24 Jun '12

Hi, How wil i get the stored user name in galaxy .I want to use this name in mako page.I am modifying my local instance of galaxy. Regards shashi ------------------------------------------------------------------------------------------------------------------------------- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. -------------------------------------------------------------------------------------------------------------------------------

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tool_data_table_config.xml.sample
by Birgit Crain 22 Jun '12

22 Jun '12

Hi I'm developing tools that use an entry in the tool_data_table_config.xml file. For upload into a repository I created a tool_data_table_config.xml.sample file with the corresponding table entry. The structure for the file I copied from the tool_data_table_config.xml. in the galaxy download. <tables>  <table name="cg_crr_files" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/cg_crr_files.loc" /> </table>  </tables> When I upload the tar ball into the repository the tools won't load properly and I get the following message: not well-formed (invalid token): line 1, column 0 Any suggestions what I'm missing or how to fix this error? Thanks, Birgit ________________________________ The contents of this e-mail and any attachments are confidential and only for use by the intended recipient. Any unauthorized use, distribution or copying of this message is strictly prohibited. If you are not the intended recipient please inform the sender immediately by reply e-mail and delete this message from your system. Thank you for your co-operation.

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tool_conf.xml and toolbar ordering
by Robert Chase 22 Jun '12

22 Jun '12

Hello, We are trying to perfect some of the details of our tool bar. Some new sections we created and added to the beginning of the tool_conf.xml file appear at the bottom of the tool bar. Do we have to do something to get galaxy to reload the tool bar from scratch? -Rob

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Local jobs aren't dispatching in a balanced configuration deployed on a cluster
by Dorset, Daniel C 22 Jun '12

22 Jun '12

I have galaxy running on my institution's cluster computing service, which uses PBS. It's in a balanced configuration. Jobs going to the cluster submit without any problem at all. However, any job that I have specified to run locally in the universe_wgsi.ini file won't dispatch. There isn't any record of the job in the manager.log, or any of the handler[#].log files. In fact, I've never seen anything in the handler logfiles after "serving on [GALAXY IP]:[SPECIFIC PORT NUMBER OF HANDLER]". The manager logfile has all the details about the jobs dispatched to the pbs runner, but nothing about local jobs. HOWEVER, if I stop Galaxy using "GALAXY_RUN_ALL=1 sh ./run.sh --stop-daemon" and restart using "GALAXY_RUN_ALL=1 sh ./run.sh --daemon" then the local jobs that were waiting to run begin immediately. Information about them shows up in manager.log, but not in the handler0.log or handler1.log files. I'm on an 8-core Dell R410 server, if that matters. The server portion of my universe_wsgi.ini file is pasted below. # ---- HTTP Server ---------------------------------------------------------- # Configuration of the internal HTTP server. [server:web0] # The internal HTTP server to use. Currently only Paste is provided. This # option is required. use = egg:Paste#http # The port on which to listen. port = 8080 # The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. host = localhost # Use a threadpool for the web server instead of creating a thread for each # request. use_threadpool = True # Number of threads in the web server thread pool. threadpool_workers = 7 [server:web1] use = egg:Paste#http port = 8081 host = localhost use_threadpool = true threadpool_workers = 7 [server:manager] use = egg:Paste#http port = 8079 host = localhost use_threadpool = true threadpool_workers = 5 [server:handler0] use = egg:Paste#http port = 8090 host = localhost use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8091 host = localhost use_threadpool = true threadpool_workers = 5 [app:main] # -- Application and filtering job_manager = manager job_handler = handler0,handler1 # ---- Custom Parameters ----------------------------------------------------

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Applications open for GMOD Summer School 2012
by Scott Cain 22 Jun '12

22 Jun '12

Applications are now being accepted for the 2012 GMOD Summer School course, a five-day hands-on school aimed at teaching new GMOD administrators how to install, configure and integrate popular GMOD Components. The course will be held August 25-29 at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina. https://docs.google.com/a/scottcain.net/spreadsheet/embeddedform?formkey=dG… These components will be covered at the school: Apollo or WebApollo - genome annotation editor Chado - biological database schema Galaxy - workflow system GBrowse - genome viewer GBrowse_syn - synteny viewer GFF3 - genome annotation file format and tools InterMine - biological data mining system JBrowse - next generation genome browser MAKER - genome annotation pipeline Tripal - web front end to Chado databases The deadline for applying is the end of July 9, 2012. Admission is competitive and is based on the strength of the application, especially the statement of interest. The 2011 school had over 70 applicants for the 25 slots. Any application received after deadline will be automatically placed on the waiting list. The course requires some knowledge of Linux as a prerequisite. The registration fee will be $300 (only $60 per day). There will be a limited number of scholarships available. Thanks, Scott Cain -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

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Workflow API (runtime modification of tool parameters)
by Richard Park 21 Jun '12

21 Jun '12

Hello, I was wondering what would be the best way to extend Galaxy's API functionality to allow for runtime modification of tool parameters? I have successfully been able to run workflows programmatically using the API, following the basic steps in: scripts/api/execute_workflow.py. scripts/api/example_watch_folder.py However, it is unclear to me, what would be the best way to run workflows through API with specific parameters at various steps. Should I generate new workflows for every workflow that requires different parameters and upload this to galaxy? Or would it be better to extend the API to allow for runtime parameter configuration? If this is the case, any pointers on how to extend this would be greatly appreciated. Thank you, Richard Park

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API calls randomly selecting files upon submission
by Anthonius deBoer 21 Jun '12

21 Jun '12

Hi, I have a very bizarre problem with Galaxy. I have to run a workflow through the API, since Galaxy cannot deal with many pair-end FASTQ files... In the past I had no issues with this and it always run as expected. But in the last few days when I select 2 FASTQ files to be run in with the API, invariably Galaxy chooses a completely different set of files to run the workflow on... I double checked that I find the right file throug the API and that the ID's are correct and that those ID's are indeed pointing to the right files, but once I pass the MAP to Galaxy, it randomly chooses some file... Not sure how to test this further..(Using the latest pull from galaxy_central, database @101) Here's some logs from my tool (not going to help a lot I think) Getting GALAXY configuration settings... Found FASTQ library: ONCOMED_TEST Found Workflow: MUT190-1 PE DNA_SEQ - Trimmomatic-BWA-REALIGN-DEDUP-VCF (GRCh37-DECOY) Found history prefix: ONCOMED-BAKEOFF Found Galaxy URL: http://srp106:8080/api [OK] ------------------------------------------------------------------- DISPLAY.py output for the two files I want to run...But different files were run in the WF ----------------------- Getting FASTQ files from the library... {'/2_181_3_CTTGTA_R1.fastq': '11049d6355c1fae6', '/2_181_3_CTTGTA_R2.fastq': '2172873b78ef3de8'} [OK] Found 2 FASTQ files ------------------------------------------------------------------- Retrieving workflow step definitions... TARGETS (GATK) -> ONCOMED/Baits and Targets/SS_OM_v1_targetsOM.gatk-interval [OK] BAITS -> ONCOMED/Baits and Targets/SS_OM_v1_baitsOM.interval [OK] COSMIC Dataset -> Annotations/CosmicMutantExport_v56_151111.vcf [OK] Mills_and_1000G_gold_standard -> Annotations/Annotations used in GATK-1.5/Mills_and_1000G_gold_standard.indels.b37.sites.vcf [OK] Adapters File -> Annotations/Adapters.fasta [OK] TARGETS -> ONCOMED/Baits and Targets/SS_OM_v1_targetsOM.interval [OK] dbSNP VCF File -> Annotations/Annotations used in GATK-1.5/dbsnp_135.b37.vcf [OK] TARGETS400 (GATK) -> ONCOMED/Baits and Targets/SS_OM_v1_targetsOM_PLUS400.gatk-interval [OK] ------------------------------------------------------------------- Preparing workflow for : /2_181_3_CTTGTA_R1.fastq Response -------- {'outputs': ['685cc0daf312e1e2', '5faa831fd7938831', '31b4c60b45b51900', '55dec7d4d8038078', '8b4bd251f4acfdb2', '991643c8bf045bdf', '45509d1f3c223d75', '69ee8e65832b0a48', '1d42f64460defe7a', 'c58ddab89b2bb805', '8bfc64bb47770912', 'f204dc7bb5ecfc2e', 'cde9aa04cfe839d1', '6362db4d5959d831', 'c01d9ed9facb9b70', '8a6baaaff54e1b05', '3842cee51a54bc8a', 'a1c8e68fee33b3f4', '7780674a8a538878', '32baf3117f18f4a9', 'd81e438f0fefa4fe', '37291cf3d6fd439a', '9b0ffea8ff1d4477', '8be5b6d3aeb85faf', 'b7c76befdaa37432', 'ffcf2e98e3761238', '900232bec5f8fcbe', 'acb2c56b985cec44', '7f15aaa8ca46161f', 'bb8f19f6facd93af', 'f9c244896d5b57dc', '8512f4fc5aed6ea7', '3f52c44d599b9716', '55806ff905fd6286', '0cb88461cff7d031', 'a273ec073a5ae9a6', 'b4fecb3654146377', '9931773a693bd74d', 'da97567b301b6e88', 'db19f117b9ba1f38', '6e9cefcf946aa2eb', '32b7a1d98d5ba938', '950b17b0eeebc8ce', 'c46ef25bdd0b128c', 'd2d71b57d04fdf56', '99ad472ce159d2b4', 'c2a0592a7bfde32d', 'cd476a668e76e2fd', '610abd782fd87335', 'f65cfa41776c8092', '33a09f65ad37eefb', '6a4013fe7480be2e', '0161b00ac62dd980', '177fef443e7d000a', '093d5543780988ae', '603db5a5490d658a', '5e639ad0ecdbbfaa', '601406f579c6cccc', '318bdcc79e1698f5', '9e0a3f75c768292a', '4a913b7f86293e50', '0edd411e46492187', '270afa41507f14e5', '4b75e21d1ac0d2ad', '1816e3ba5ffa42d6', '71b643cde9fb710c', '62d1d0058327a5da', '133576f2dda5c2b4', '450c3dc15a3aa0a0', '5e747c660af21e40', '7db0323336d28301', '9878576367d5f544', 'b150a412957324a5', 'e97867c104e59e02', 'c8e9faf4b8a01e67', '5d194649d99822eb'], 'history': '31d04ac4a1e13563'} ---------------------- Member Information ------------------ ldda_id: ccfcc222604b2175 misc_blurb: 14.3 Gb name: 2_181_3_CTTGTA_R2.fastq data_type: fastq file_name: /mnt/ngs/data/ProcessedData/Casava_builds/SEQUENCER02/120608_SN402_0181_AD143FACXX/fastq/2_181_3_CTTGTA_R2.fastq uploaded_by: tdeboer(a)genomichealth.com metadata_sequences: None template_data: {} genome_build: hg19-decoy model_class: LibraryDataset misc_info: uploaded fastq file file_size: 15361395563 metadata_data_lines: None message: id: 2172873b78ef3de8 date_uploaded: 2012-06-21T17:37:20.383314 metadata_dbkey: hg19-decoy (galaxy_env)[tdeboer@srp106 api]$ myDisplay.py libraries/fb85969571388350/contents/11049d6355c1fae6 Member Information ------------------ ldda_id: 6768e90755e11e63 misc_blurb: 14.3 Gb name: 2_181_3_CTTGTA_R1.fastq data_type: fastq file_name: /mnt/ngs/data/ProcessedData/Casava_builds/SEQUENCER02/120608_SN402_0181_AD143FACXX/fastq/2_181_3_CTTGTA_R1.fastq uploaded_by: tdeboer(a)genomichealth.com metadata_sequences: None template_data: {} genome_build: hg19-decoy model_class: LibraryDataset misc_info: uploaded fastq file file_size: 15361395563 metadata_data_lines: None message: id: 11049d6355c1fae6 date_uploaded: 2012-06-21T17:37:19.122245 metadata_dbkey: hg19-decoy Thanks, Thon

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migrate ownership of galaxy user
by David Hoover 21 Jun '12

21 Jun '12

I have a somewhat unusual problem. I have a local instance of Galaxy wherein users are created automatically upon authentication (use_remote_user = True). However, for a handful of users, their remote_user names have changed. After that change, a new Galaxy user and role were created, and they can't access their old data. Worse, they continued using the new account and so now have two sets of (possibly) identical data. Is there a simple way of migrating datasets, jobs, quotas, etc., from one user to another? I've figured out a way to make the necessary changes at the MySQL database level. However, there is one sticky problem. None of the tables (aside from role and galaxy_user) define the role_id or the user_id as unique, so I would assume I can simply UPDATE the table to set the old role_id or user_id to the new role_id or user_id. Unfortunately, it appears that some of the tables are in practice keeping the role_id or user_id as unique. For example, default_user_permissions or user_role_association. Could a single user have multiple default permissions or multiple roles? What would happen if this were the case? In short, can anyone say which tables have practical unique role_id/user_id to data associations? Of course, I could just delete the old user and say too bad... Thanks, David Hoover Helix Systems Staff, CIT/NIH

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Few questions about first time out with local install
by Alan V. Cowles 21 Jun '12

21 Jun '12

Hey guys, I just recently got several inquiries from users who would like to set up a local galaxy instance here at our university. I setup a server and got it basically running, the only modifications I have made thus far, are opening the website outside of localhost, and having it communicate with our central postgres server. I have two questions I am hoping someone can answer, I have spent some time on a few blogs and through the archive and haven't found an exact answer. My first question: Is there a way to make the galaxy server retrieve data from a local storage set, instead of uploading newly through the web interface? Http seems like an awfully inefficient way to transmit sequence data. If I mounted an nfs directory full of sequence to the server could I load and analyze it, and what options would I do to config this? My second question: When setting up a cluster do most people make the galaxy server a head and farm out to compute nodes, or do you send jobs off to a remote cluster entirely? It seems like the options in the universe_wsgi.ini file calls a local daemon for cluster management, but I am a bit confused. I hope I haven't wasted anybodies time with these questions. This tool looks amazing and our researchers are keen to get going at it. AC

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Problem with proxy
by SHAUN WEBB 21 Jun '12

21 Jun '12

Hi, I have set up a test version of Galaxy running on the same hostname as our production server. I have set up the test version to include web scaling and to run behind a proxy served on a sub-directory. The production version has neither of these features. When I enable the following code in universe.wsgi.ini I am unable to login. There is no error, also I cannot access a history if I try to upload datasets as an anonymous user, again there is no error but datasets do not appear in the history: [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy_test [app:main] filter-with = proxy-prefix cookie_path = /galaxy_test The cookie_path code appears to be causing the issue. Is the problem having 2 instances on the same hostname and only one behind a proxy? If I comment out the code everything seems to work okay (apart from the problem I had previously http://gmod.827538.n3.nabble.com/Error-loading-data-tt4013269.html) Thanks in advance for any help Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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