April 2013 - galaxy-dev - lists.galaxyproject.org

gene annotation file (gtf)
by Hagai Cohen 04 Apr '13

04 Apr '13

Hi, Is is possible to configure gene annotation file files inside galaxy per genome internally? As in bowtie indices or something similiar. I don't want to upload the ucsc constant gtf files on each history I need them. Thanks for the help, Hagai

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Re: [galaxy-dev] How to show alert message to user when running a tool in galaxy
by Peter Cock 04 Apr '13

04 Apr '13

On Thu, Apr 4, 2013 at 3:23 PM, BingXin Lu <soulsophia(a)gmail.com> wrote: > Thanks a lot, it is a solution. However, I think it is more user-friendly to > give user instant prompt when detecting conflict in the database, so that > user can decide to override current record in the database or keep > current record and stop running the tool again. I'm not aware of anything like that being done via the <param>'s <validator> tag... but that is the appropriate place for any checks on a parameter before the execute button is pressed. Peter P.S. Don't forget to include the mailing list in replies.

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How to show alert message to user when running a tool in galaxy
by BingXin Lu 04 Apr '13

04 Apr '13

Dear all, I have added a tool in galaxy. After clicking 'Execute', this tool will query an external database for some information to ensure that there are no conflict records in the database. So sometimes an alert message should be sent to user if there are wrong records in the database. But I have not found out an efficient way to implement this in galaxy. I am wondering if it is possible to give some warning message to users when running a tool in galaxy and how to do it if it is feasible. I implemented the tool with an xml file and a python file. I am wondering calling javascript from the python code to give user error information. But it seems infeasible and I do not know where to start. Do you have any ideas? Thank you very much! Best regards, --Bingxin

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Is there a way to determine if a tool was run from the UI or from a Workflow step?
by Anthonius deBoer 04 Apr '13

04 Apr '13

Hi, I would like to allow interactive use of the Galaxy UI to be run in a different "destination" from a tool that is run from a workflow... I am looking into setting up the dynamic running method in jobs_conf.xml and a special dynamic function I am defining, but not too sure how I can determine (if this is even possible) if a tool is run as part of a Workflow step or if it was run interactively.... Any pointers? Thanks

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Example for DRMAA in new jobs_conf.xml example file incorrect. It's "DRMAAJobRunner" not "DRMAARunner"
by Anthonius deBoer 04 Apr '13

04 Apr '13

It seems that the examples in the jobs_conf.xml file incorrectly defines the DRMAA runner as galaxy.jobs.runners.drmaa:DRMAARunner which should be galaxy.jobs.runners.drmaa:DRMAAJobRunner It's really unhelpful if a major change to the way things are run contains these kinds of issues/bugs in the examples, since there is not much on the wikki pages on what are the pre-defined runners...... I had to dig down in the code to figure out the DRMAA runners name... Hope this helps others getting DRMAA to run in Galaxy after this major update... Thon

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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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