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

What image formats can be displayed in the Galaxy view panel?
by Luobin Yang 07 Feb '13

07 Feb '13

Hi, I tried the pcx and ps formats, but the browser just downloads these kinds of files instead rendering them in the Galaxy window... It seems png and pdf files can be rendered in the Galaxy windows. How can I make Galaxy display other image formats like ps and pcx? Thanks, Luobin

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workflow intermediate files hog memory
by mark.rose＠syngenta.com 07 Feb '13

07 Feb '13

Hi All Intermediate files in a workflow often make up the large majority of a workflow's output and, when this is an NGS analysis, this volume can be HUGE. This is a considerable concern for me as we consider implementing a local install of galaxy. Storing all of this seems useless (once workflow has been worked out) and a huge memory hog if one wants to actually persist the useful final outputs of workflows in galaxy. Is there any way to specify that the output of particular steps in a workflow be deleted (or sent to /tmp) upon successful workflow completion? How are others dealing with this? Is it inadvisable to use galaxy to serve as a repository of results? Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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Re: [galaxy-dev] card 79: Split large jobs over multiple nodes for processing
by Alex.Khassapov＠csiro.au 07 Feb '13

07 Feb '13

Hi All, Can anybody please add a few words on how can we use the “initial implementation” which “ exists in the tasks framework”? -Alex From: Trello [mailto:do-not-reply@trello.com] Sent: Wednesday, 6 February 2013 10:58 AM To: Khassapov, Alex (CSIRO IM&T, Clayton) Subject: 4 new notifications on the board Galaxy: Development since 5:56 PM (Tuesday) [https://trello.com/images/logo-s.png] Notifications ________________________________ On Galaxy: Development<https://trello.com/board/galaxy-development/506338ce32ae458f6d15e4b3> [https://trello-avatars.s3.amazonaws.com/a6e93a63989ab71cd87ade0165a04b08/30… Taylor added [https://trello-avatars.s3.amazonaws.com/d0f1bba8eb293d305140421271c383a9/30…] Dannon Baker to the card 79: Split large jobs over multiple nodes for processing<https://trello.com/card/79-split-large-jobs-over-multiple-nodes-for-process…> on Galaxy: Development<https://trello.com/board/galaxy-development/506338ce32ae458f6d15e4b3> [https://trello-avatars.s3.amazonaws.com/a6e93a63989ab71cd87ade0165a04b08/30… Taylor commented on the card 79: Split large jobs over multiple nodes for processing<https://trello.com/card/79-split-large-jobs-over-multiple-nodes-for-process…> on Galaxy: Development<https://trello.com/board/galaxy-development/506338ce32ae458f6d15e4b3> An initial implementation exists in the tasks framework. [https://trello-avatars.s3.amazonaws.com/a6e93a63989ab71cd87ade0165a04b08/30… Taylor moved the card 79: Split large jobs over multiple nodes for processing<https://trello.com/card/79-split-large-jobs-over-multiple-nodes-for-process…> to Complete on Galaxy: Development<https://trello.com/board/galaxy-development/506338ce32ae458f6d15e4b3> [https://trello-avatars.s3.amazonaws.com/a6e93a63989ab71cd87ade0165a04b08/30… Taylor moved the card 137: allow multiple="true" in input param fields of type data<https://trello.com/card/137-allow-multiple-true-in-input-param-fields-of-ty…> to Pull Requests / Patches on Galaxy: Development<https://trello.com/board/galaxy-development/506338ce32ae458f6d15e4b3> Change how often you get email on your account page<https://trello.com/my/account>. Follow Trello on Twitter<https://twitter.com/intent/follow?user_id=360831528> and Facebook<https://www.facebook.com/TrelloApp>. Get the Trello app for iPhone<http://itunes.com/apps/trello> or Android<https://play.google.com/store/apps/details?id=com.trello>.

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Import history from web server to local server
by julie dubois 07 Feb '13

07 Feb '13

Hi all, I'm trying to import an history from the web server to my local server. First I've chosen "Export to File" in the history menu and I've seen a message with an url. Second in my local server I've created a new history and I chosen "Import from File" in my new history menu. I've pasted the url in the formular and A message says : "Importing history from ' http://cistrome.org/ap/history/export_archive?id=################'. This history will be visible when the import is complete" But there is nothing in my new history and it seems that no operation is running!!! Is it normal? Another idea to transfer an hitory and his datasets in another history? Thanks. julie

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Re: [galaxy-dev] Why "upload" to Local Instance rather than "import"?
by Jennifer Jackson 07 Feb '13

07 Feb '13

Hi Greg, I believe that you do not need to actually copy the data to your workstation (although you could ...) - instead, symbolically link it from the external drive to your workstation so that it appears local. Then upload from that path. The data library upload "by path" option will follow a single symbolic link to data. This is explained in much more detail in our wiki, please see the section "Upload directory of files": http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles Sorry for the late reply - this email got sorted incorrectly - it really is best to either send replies back to the mailing list or to start over with a new thread (brand new message "to" list only, not just a reply with a new subject line). This ensures we get your question tagged and tracked - and you benefit from all the helpful developers on this list that know more than I about many technical things Galaxy. If anyway else has suggestions for Greg, please feel free to add to the post, Jen Galaxy team On 2/4/13 12:53 PM, Thyssen, Gregory - ARS wrote: > Hi Jen, > > I have a local instance of Galaxy running on my workstation. > > I have external hard drives full of fastq sequencing files. > > I want to make them available to myself as data libraries. I am the > Admin and sole user at this point. > > The “upload” data libraries seems to pass the data through the (slow) > network, even though my workstation and external hard drives are linked > by USB. > > What is the fastest way to import my files into my galaxy instance? Can > I copy them into some folder on the workstation’s hard drive? > > Since everything is physically connected, I don’t think I should be > limited by my network speed. > > Thanks, > > Greg Thyssen > -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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No peek and no column count in history items
by graham etherington (TSL) 07 Feb '13

07 Feb '13

Hi, Some of our users are experiencing problems with (mainly) tabular data on our local install of Galaxy (changeset 8368:0042b30216fc, Nov 06 2012). I'm presuming it's some kind of meta-data problem. The first strange behavior is that they are getting green history items, but when the history item is expanded it has 'no peek' in the data preview and 'empty' as the line-count. When they click on the eye icon, their data appears and the output is as expected. Sometimes the data preview panel (in the history item) has the number of columns across the top of it (but still with 'no peek') and this data can be used downstream, but often the columns are missing or incorrect and although the output file is correctly tabulated, it cannot be used downstream. All of these problems can be addressed by using the Auto-detect in the Edit Attributes. This provides the correct column count, gives the line count and provides a peek. This happens with lots of different tools, usually (but not exclusively) with tabular data. I'm wondering if anyone has ever encountered this problem before and what they did to address it. Many thanks, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601

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VirtualEnv
by Thyssen, Gregory - ARS 07 Feb '13

07 Feb '13

Hello Everything seems to be working on my local Galaxy I was talking to my IT guy who did the initial installation and he said that virtualenv may not have been loaded. When he did % yum install python-virtualenv.noarch He got a not found error. He did install mercurial and then completed the Install instructions from www.biocodershub.net/community/guest-post-notes-on-installing-galaxy/<http://www.biocodershub.net/community/guest-post-notes-on-installing-galaxy/> What should we do at this point? Is VirtualEnv dispensible? What should I expect to be broken? Whats the fix? Thank you, Gregory Thyssen, PhD Molecular Biologist Cotton Fiber Bioscience USDA-ARS-Southern Regional Research Center 1100 Robert E Lee Blvd New Orleans, LA 70124 gregory.thyssen(a)ars.usda.gov 504-286-4280 This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

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Divide the web interface into sections for a tool.
by Luobin Yang 06 Feb '13

06 Feb '13

Hi, Galaxy developers, I would like to have the parameters on the web interface to be packed into sections for a tool. Is there a way to do this? There is a <page> tag, but the document says we should avoid using it. Also there is no replacement tag for <page>. The problem using the <page> tag is that there seems missing a "previous step" button on the pages other than the first page. If there is a section tag to be rendered as a box with a title and all the tags inside that section are rendered inside the box, that would be great. Even a horizontal bar to separate the sections is helpful. Thanks, Luobin

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galaxy error
by Jennifer Jackson 06 Feb '13

06 Feb '13

Hi Bassam, First, I am going to post your question to the galaxy-dev(a)bx.psu.edu mailing list. This is where local and cloud install Galaxy questions can get the best exposure to the development community. Next, this isn't necessarily an error. And was the full line really this? nohup: ignoring input and redirecting stderr to stdout This is more of a linux issue than a Galaxy issue, but I'll give some feedback and others can comment as well (or a google will bring up many threads on the topic). Basically, this is just a stderr warning and can be ignored. IF you should be using it - nohup isn't for all jobs. Personally, I use it for data processing sometimes (general use, not part of running Galaxy), but I think I am the only one (here!), since there are other options to keep processes detached from individual sessions. It is a habit. I see this all the time and the job keeps on running. I could redirect the stderr to /dev/null but I usually just ignore it (lazy = type less characters). But I don't admin our Galaxy server either and wouldn't consider using it for that purpose. Which is why I am posting to the mailing list, where the admins can comment. On your system, the process might have actually run - this message has nothing to do with it running or not. But you want to be careful - if the process is interactive (requires a password), you don't want to use nohup and redirect both stdout and stderr. I don't know what command you ran, but you can do a few things to check to see if the process is running: See if the nohup.out file is keeping a log of some sort of the job (if it is still running, or if it quit and put output here): $ more nohup.out See what jobs are running in the current session: $ jobs See what jobs are assigned to the Galaxy user, you can do something like: $ ps -u galaxy Check to see if what you asked the process to do has been done, or check the other galaxy logs for activity along those lines. I am not sure if this is helpful or not, but perhaps will point you in the correct direction (linux command help/usage) where you can find out more. Take care, Jen Galaxy team On 2/6/13 11:24 AM, Bassam Tork wrote: > Dear Jennifer, > When I ran galaxy on our server it gave the error: > > nohup: ignoring input > > although I provided all inputs > Appreciate your help. > -- > Bassam Tork. -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Job handler : crash
by Christophe Caron 06 Feb '13

06 Feb '13

Hello, We run Galaxy (2013 January version) with load balancing mode (5 x web manager, 5 job handler) with Apache/Sun Grid Engine 6.0u4/CentOS 6.3 - Since 2 weeks, some handler job process crash during the Galaxy startup with this error message in handlerx.log ..... Starting server in PID 13634. serving on http://127.0.0.1:8091 galaxy.jobs.handler DEBUG 2013-01-29 20:06:48,902 Stopping job 22842: galaxy.jobs.handler DEBUG 2013-01-29 20:06:48,902 stopping job 22842 in drmaa runner - The system log files report a segfault with libdrmaa kernel: python[13977]: segfault at 0 ip 00007f2811805dc5 sp 00007f27f4aac0a0 error 4 in libdrmaa.so.1.0[7f28116dd000+185000] Thanks for your help ! Christophe -- Christophe Caron Station Biologique / Service Informatique et Bio-informatique Place Georges Teissier - CS 90074 29688 Roscoff Cedex Analysis and Bioinformatics for Marine Science http://abims.sb-roscoff.fr/ christophe.caron(a)sb-roscoff.fr tél: +33 (0)2 98 29 25 43 / +33 (0)6 07 83 54 77

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