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Re: [galaxy-dev] [galaxy-bugs] Error message when trying to dowload Manhattan plot using the web version
by Christos Kannas 04 Apr '13

04 Apr '13

Hi, Regarding the broken download of a composite datatype, as i have commented in https://trello.com/c/25OfmDa1, is due to the temporary folder permissions, where the archived composite datatype is store for download, are set to 0700 and is should be at least 0664, so that the web server can read its contents. The change I've made on our local instance of Galaxy is the following: (We are using galaxy-dist release_2013.02.08) lib/galaxy/datatypes/data.py @@ -215,19 +215,21 @@ if (params.do_action == 'zip'): # Can't use mkstemp - the file must not exist first tmpd = tempfile.mkdtemp() - tmpf = os.path.join( tmpd, 'library_download.' + params.do_action ) + # Change permissions of temp folder + os.chmod(tmpd, 0775) + tmpf = os.path.join(tmpd, 'library_download.' + params.do_action) Kind regards, Christos -- Christos Kannas Researcher Ph.D Student e-Health Laboratory <http://www.medinfo.cs.ucy.ac.cy/> kannas.christos(a)ucy.ac.cy kannas.christos(a)cs.ucy.ac.cy chriskannas(a)gmail.com Mob: (+357) 99530608

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(no subject)
by auguste aurelie 04 Apr '13

04 Apr '13

Dear Galaxy manager, I'm using the GATK beta version on your Galaxy website. I'm little bit concerned by the fact that i cannot choose my reference genome, either in the "depth of coverage" or in the "realigner target creator". I want to use the Hg19 genome, but i do not know how to load it. Can you help me please? Thanks -- *AUGUSTE Aurélie* Post doctorante Génétique et génomique du développement gonadique Université Paris-Diderot/Paris 7 Institut Jacques Monod CNRS-UMR 7592 555B - Bâtiment Buffon 15 Rue Hélène Brion Paris Cedex 13 France. Phone: 0033 1 57 27 81 17

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Re: [galaxy-dev] Toolshed errors
by Greg Von Kuster 03 Apr '13

03 Apr '13

Hello Björn, Thanks very much for your message! Please see my inline comments. On Apr 2, 2013, at 4:33 PM, Björn Grüning wrote: > I have tested a few things regarding to the toolshed and prepared a > complex module-dependency-beast, with meta-package and > orhphan-tool-dependencies and so on. A few problems I encountered are > summarized below. You can try it by yourself, if you install the > chemicaltoolbox package from the testtoolshed. > > - three crashes with traceback attached, during tool-installation > > - one 'name' not defined error, with attached patch Thanks very much for finding this issue and for the patch. We've applied it in changeset 9252:da2d6ee29f30 in our stable branch, so it is running on both public Galaxy tool sheds. > > - For me the the installation of tools with really complex and long > compiling steps are stalled in 'Installing' forever. Try to install the > osra package (it often hangs, but not every time). > Its not possible to uninstall/reinstall these dependencies > without touching the database. And the error says, tool is already > installed. Would be nice if the admin is able to reset that repository > easily, even if it is limbo ... (is there a timeout somewhere?) > Error: paste.httpserver.ThreadPool WARNING 2013-04-02 22:02:41,256 Thread 140246687659776 hung (working on task for 1964 seconds) > (The SystemExit: traceback attached) I've create the following Trello card for this issue: https://trello.com/card/toolshed-enable-galaxy-admin-to-reset-tool-dependen… There are 4 places where this timeout may be occurring: Galaxy tool shed server, Galaxy tool shed nginx, a proxy server at your end, or your local Galaxy server. There is not enough information in your attached traceback log to determine where the timeout is occurring. Can you provide me your Galaxy server's IP address so I can look in logs at our end? > > - It would be great if the tool-developer or the admin has more control > over the location of the tools in the toolbar. Installing meta package > leaves you with only one choice, regardless how many tools are bundled. Support for this will be available in the next Galaxy release. There are Trello cards for this here: https://trello.com/card/toolshed-enhance-the-current-galaxy-api-for-install… https://trello.com/card/toolshed-add-features-that-leverage-the-galaxy-api-… > > - Installing dependencies will leave me with empty folders under > galaxy-root with the name of the dependency. My guess is, > that if I manually download a file/folder with wget, the folder is not purged, but the content is. Our intent is that installing repositories from the tool shed is completely automated with no manual intervention required. Tool dependency definitions should not use utilities like wget to download dependencies because these utilities may not be available in the environments (e.g. vanilla mac os) into which the repositories are being installed. I'll enhance the tool dependency tag sets as necessary to accommodate additional download and install requirements. Can you let me know if the current download_by_url needs enhancements? > > - Often after upgrading the tool_dependencies.xml file, I was not able > to 'get updates' from the toolshed. The version was up-to-data, but it > wasn't. Deinstalling and Installing fixed it. But I think its ab bug, > isn't it? This very well may be a bug. Can you please provide additional details so that I can reproduce this behavior? I'll get a fix asap. > > - Is there a way, to just download a python file, not zipped and add it to PYTHONPATH? > If I download it with <action type="download_by_url"> I have problems to copy that file with move. > I would like to download it with wget, but one download by URL is required. My current solution is, > to include a dummy download_by_url and than fetch with wget, or download a archive version. I've created the following Trello card for this issue: https://trello.com/card/toolshed-enhance-the-download-by-url-process-for-in… > > - Is it correct that a repository referenced only in > tool_dependencies.xml is not enough to install? numpy was only > referenced as tool_dependency and I got the error that the tool (with > owner and revision) was not found. After adding to repository_dependency > it was ok. Can you provide more details about your question above (e.g., the tool_dependencies.xml fie would help). I want to make sure i understand the issue. Thanks very much Björn, Greg Von Kuster

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Cancel running jobs/workflows through API
by Richard Park 03 Apr '13

03 Apr '13

Hey guys, I know there's no current way of canceling jobs or workflows through the API, but does anyone have any idea on how to implement this in Galaxy? i.e. where in the code base to see how galaxy is currently killing jobs. My ideal solution would be to get the list of qeued jobs for a giving history and call something to kill all running jobs in a history or a way of iterating through all jobs. Any help would greatly appreciated, thanks, Richard

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Galaxy - FTP Download Problem
by Rob Leclerc 03 Apr '13

03 Apr '13

We have a CloudMan Galaxy install on Amazon and I'm able to upload FTP files from FireZilla (or programatically through a Java service I wrote). However, I'm unable to download that same file once uploaded. The 550 response is a "Requested action not take. File unavailable (e.g., file not found, no access). I have rwx permissions on the directory and rw permissions on the file.* * * * *Status:* Starting download of /TAF1_ChIP-2.txt *Command: *TYPE A *Response:* 200 Type set to A *Command: *PASV *Response: *227 Entering Passive Mode (10,40,11,236,117,50). *Status: *Server sent passive reply with unroutable address. Using server address instead. *Command: *RETR TAF1_ChIP-2.txt *Response: *550 TAF1_ChIP-2.txt: Operation not permitted *Error: Critical file transfer error* Thoughts? Cheers, Rob

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REST API
by Marc Logghe 02 Apr '13

02 Apr '13

Hi, I was trying to run workflows from the command line using workflow_execute.py in /scripts/api. According to the documentation, the commandline should look like: python workflow_execute.py <api_key> <galaxy_url>/api/workflows f2db41e1fa331b3e 'hist_id=a912e9e5d84530d4' '38=hda=03501d7626bd192f I understand that 'hda' refers to the src of the input data, in this case being the history. However, it is not clear to me what 38 is actually referring to. Is it the step number ? Is it the id shown in the JSON response code of <galaxy_url/api/workflows/<workflow id> ? E.g "535" in: {"url": "/galaxy/api/workflows/f7bb1edd6b95db62", "inputs": {}, "steps": {"535": {"tool_id": "iep", "input_steps": {}, "type": "tool", "id": 535}}, "id": "f7bb1edd6b95db62", "name": "test_workflow"} What is "inputs" and why is its value empty {} ? If a tool step has multiple input parameters, how can you refer to the correct parameter using the 'step=src=id' syntax ? Thanks, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________

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April 2013 Galaxy Update
by Dave Clements 02 Apr '13

02 Apr '13

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Galaxy April 1, 2013 Distribution
by Jennifer Jackson 01 Apr '13

01 Apr '13

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GCC2013 Oral Presentation Abstract Submission Closes 12 April
by Dave Clements 01 Apr '13

01 Apr '13

Hello all, This is just a reminder that the *deadline for submitting an oral presentation abstract is 12 April, which is less than two weeks away*. See http://wiki.galaxyproject.org/Events/GCC2013/Abstracts The poster presentation abstract deadline is 3 May. Thanks, Dave C On Sun, Feb 24, 2013 at 7:40 PM, Dave Clements <clements(a)galaxyproject.org>wrote: > Dear Galaxy Community, > > We are pleased to announce that early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > and paper and poster abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> are > now open for the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> > . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University > of Oslo <http://uio.no/>. > > GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity > to participate in two full days of presentations, discussions, poster > sessions, keynotes, lightning talks and breakouts, all about > high-throughput biology and the tools that support it. The conference also > includes a Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> for > the second year in a row, this year with more in-depth topic coverage, more > concurrent sessions, and more topics. > > If you are a biologist or bioinformatician performing or enabling > high-throughput biological research, then please consider attending. > GCC2013 is aimed at: > > - Bioinformatics tool developers and data providers > - Workflow developers and power bioinformatics users > - Sequencing and Bioinformatics core staff > - Data archival and analysis reproducibility specialists > > *Early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > * *saves up to 75% off regular registration costs,* and is very > affordable, with combined registration (Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> + > main meeting) starting at ~ €95 for post-docs and students. Registering > early also assures you a spot in the Training Day workshops you want to > attend. Once a Training Day session becomes full, it will be closed to new > registrations. Early registration closes 24 May. > > *Abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> > * for oral presentations closes 12 April, and for posters on 3 May. > Please consider presenting your work. If you are working with big > biological data, then the people at this meeting want to hear about your > work. > > Thanks, and hope to see you in Oslo! > > The GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> > > PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> > ! > -- > http://galaxyproject.org/GCC2013 > <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://wiki.galaxyproject.org/ > -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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reducing overhead for quick jobs
by Robert Baertsch 30 Mar '13

30 Mar '13

Hi All, After changing the sleep in manager.py from 5 seconds to 0.2 seconds, the job start is very snappy. I did not touch the various sleep(10)s that don't seem to be relevant. I'm testing how long it takes to sort a short bed file in galaxy. After the fix, the problem seems to be at the end of the process. In the timeline below the gap between the job ending on the server and the client getting the update is 5 seconds. Is that a built in sleep or something else? Can I turn off metadata for tools that don't generate it? BTW: thousands of seconds are on in the manager and handler logs and should be turned on in the main.log. Rather than 2 round trips to the server. I think we need a special class of tools that run in a single round trip (like the eyeball viz). The max run time for this class of jobs should be no more than a few seconds. Is that is the roadmap somewhere? -Robert Baertsch UC Santa Cruz https://medbook.ucsc.edu RUN1 - 9 seconds (1 sec to start, 0.2 sec to run , 2 sec metadata, 5.5 secs to update client) 12:08:12.? main: log job on main thread 12:08:12.8 manager : galaxy.jobs.manager DEBUG 2013-03-30 12:08:12,867 (2308) Job assigned to handler 'handler2' 12:08:13.26 handler: start handler 12:08:13.35 handler: job dispatched 12:08:13,44 handler: job runner started 12:08:13,72 handler: python tool started 12:08:13,91 handler: python tool finished 12:08:13,98 handler: set_metadata.sh started 12:08:15,70 handler: metadata ended 12:08:15,85 handler: job Ended 12:08:21 main: /api/histories - update on client RUN2 - 9 seconds (1.8 sec to start, 0.2 sec to run, 2 sec metadata, 4.5 sec to update client) 12:23:00.? main: log job on main thread 12:23:00,60 manager : galaxy.jobs.manager DEBUG 2013-03-30 12:08:12,867 (2308) Job assigned to handler 'handler2' 12:23:01,63 handler: start handler 12:23:01,72 handler: job dispatched 12:23:01,81 handler: job runner started 12:23:02,44 handler: python tool started 12:23:02,64 handler: python tool finished 12:23:02,72 handler: set_metadata.sh started 12:23:04,64 handler: metadata ended 12:23:04,71 handler: job Ended 12:23:09 main: /api/histories - update on client

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