April 2011 - galaxy-dev - lists.galaxyproject.org

Launching multiple jobs using one tool form with multiple selected datasets
by Leandro Hermida 28 Apr '11

28 Apr '11

Hi everyone, I was wondering what would be the way in Galaxy to program the following: - User clicks on a tool and form is displayed - They use a select multi menu in the form to pick lets say X multiple datasets from their history - When they click submit the tool launches X number of jobs in the history, on for each of the datasets selected. I have a common use case where users have to manually run the same tool over and over again with the same parameters for each dataset of interest in their history. I would be great to be able programmatically or otherwise with Galaxy to be able to use one form and multi select the datasets and then launch the parallel jobs in one go. regards, Leandro

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Does REMOTE_USER have to be an email address?
by Leandro Hermida 27 Apr '11

27 Apr '11

Hello, When returning REMOTE_USER env var from the external authentication method does it have to be an email address for Galaxy? The docs aren't very clear on that, in the main External Authentication section it says you have to have to set remote_user_maildomain if you aren't return an email address (and the domain will be appended it seems) but in the mod_authnz_ldap section it says you are allowed to set any attribute to return as REMOTE_USER. regards, Leandro

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Question on finding external_filename and _extra_files_path from psql DB.
by Vipin TS 26 Apr '11

26 Apr '11

Dear Galaxy Team, As a part of in-house automated cleaning of data set from our production galaxy service, I am finding difficulty to get the galaxy assigned file name (galaxy-root/database/001/dataset_001.dat) for each data set from the corresponding database. We are using PostgreSQL and when I queried through the table name called 'dataset', couldn't figure out the values for external_filename or _extra_files_path. For example: >> select * from dataset order by id DESC limit 10; id | create_time | update_time | state | deleted | purged | purgable | external_filename | _extra_files_path | file_size 70805 | 2011-04-22 20:49:55.319709 | 2011-04-22 20:50:26.643807 | ok | f | f | t | | | 421593 Could you please let me know where I can locate the file name from other tables or do I need to set up any configuration. Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany

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Galaxy Community Conference Early Registration Deadline extended to May 1
by Dave Clements 26 Apr '11

26 Apr '11

Hello all, The early registration deadline for the 2011 Galaxy Community Conference has been extended by a week, from April 24 to May 1. The conference is being held in Lunteren, the Netherlands, 25-26 May, with a special "Introduction to Galaxy" session on the evening of May 24. That's the good news. The bad news is that online registration has been taken offline, starting today, until April 26 or 27. We took this step because of unexpectedly high demand for conference centre hotel rooms on May 24 and 26. We still have ample rooms for the night of May 25,* but we are now sold out on the other nights*. We are working with the conference centre to increase our room allotment on May 24 and 26. We are optimistic of getting more rooms on May 26, but we are not as hopeful about getting additional rooms for May 24. We will reopen registration next Tuesday or Wednesday and post an update on the room situation, including alternatives, at that time. As always, please let me know if you have any questions. Thanks for your patience, Dave C. -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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Workflow variables and the workflow API
by Dave Walton 26 Apr '11

26 Apr '11

I'm working on a module that involves calling a workflow multiple times over a set of data. The workflow has a "variable" that I use for renaming output files. I see, using the workflow_execute.py example how to pass in file names, but I don't see how to pass in a value for this variable. When I do a "./display.py <api key> http://jaxgalaxydev01/api/workflows/<workflow id>" I see the two input data files I would expect, but I don't see this variable. ex: Member Information ------------------ url: /api/workflows/<workflow id> inputs: {'207': {'value': '', 'label': 'Input Dataset'}, '211': {'value': '', 'label': 'Input Dataset'}} id: <workflow id> name: Single-end RNA Seq with grooming v 2.0 (imported from uploaded file) Is there anyway to get at this variable so I can set it when I call a workflow through the API? Thanks, Dave

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galaxy related
by shashi shekhar 26 Apr '11

26 Apr '11

if i want some in information from tool xml file to code file ,how i will get the info. it it's possible ,send me detailed info. Regards galaxy user shashi shekhar

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sqlalchemy Timeout Error
by Liisa Koski 26 Apr '11

26 Apr '11

Hi, We are running many NGS workflows at the same time on our local instance of Galaxy. They are crashing with the following error Error - <class 'sqlalchemy.exc.TimeoutError'>: QueuePool limit of size 5 overflow 10 reached, connection timed out, timeout 30 In the universe_wsgi.ini we made the following adjustments: # If the server logs errors about not having enough database pool connections, # you will want to increase these values, or consider running more Galaxy # processes. database_engine_option_pool_size = 50 # this used to be 5 database_engine_option_max_overflow = 100 # this used to be 100 Those numbers were pulled out of a hat so I wanted to make sure what we were doing was correct. Is there a limit on the values? It doesn't appear to be crashing anymore but I still want to make sure. Thanks, Liisa

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galaxy after logout
by hari krishna 26 Apr '11

26 Apr '11

hi, In galaxy after logout by using browser back buttons i can able to go my home page .How to disable this facility can any one help .... -- Thanks & Regards, Hari Krishna .M

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Problem with "Map with Bowtie for Illumina" on a local Galaxy
by Leon Mei 26 Apr '11

26 Apr '11

Dear colleagues, I have a local installed Galaxy. When I try to run bowtie to align a small FASTQ file, I got the following message and the result was empty. """ empty, format: sam, database: Project-Id-Version: PACKAGE VERSION Report-Msgid-Bugs-To: POT-Creation-Date: 2008-09-21 18:33+0900 PO-Revision-Date: 2009-03-17 03:55-0400 Last-Translator: FULL NAME Language-Team: en Plural-Forms: nplurals=2; plural=(n != 1) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Generated-By: Babel 0.9.4 Info: """ It seems bowtie_wrapper.py wasn't executed at all. Has someone seen this message before and what could be the cause? Thanks, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center (http://www.nbic.nl/) Skype: leon_mei Mobile: +31 6 41709231

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Staged Method for cluster running SGE?
by Peter Cock 26 Apr '11

26 Apr '11

Hi all, So far we've been running our local Galaxy instance on a single machine, but I would like to be able to offload (some) jobs onto our local SGE cluster. I've been reading https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster Unfortunately in our setup the SGE cluster head node is a different machine to the Galaxy server, and they do not (currently) have a shared file system. Once on the cluster, the head node and the compute nodes do have a shared file system. Therefore we will need some way of copying input data from the Galaxy server to the cluster, running the job, and once the job is done, copying the results back to the Galaxy server. The "Staged Method" on the wiki sounds relevant, but appears to be for TORQUE only (via pbs_python), not any of the other back ends (via DRMAA). Have I overlooked anything on the "Cluster" wiki page? Has anyone attempted anything similar, and could you offer any guidance or tips? Thanks, Peter

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