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

Toolshed tools minimal requirments for submission
by Bossers, Alex 04 Feb '13

04 Feb '13

Hi All, We are experimenting with local toolsheds for tool maintainability. On the old galaxy wiki I can remember there was a short tutorial or small description of the minimal requirements of a tool to be submitted to the toolshed. Actually we submitted some. However we seem unable to retrieve the proper info from the updated wiki. We did find info on single tools or suites, or more special cases, but a simple example/list of how and what to include in a repository is missing (at least we cannot find it....might be an issue of wrong key words).. Anyone has an idea where to find such a document? Thanks Alex

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Behaviour of download_by_url with tar.gz during tool dependency installation
by Jean-Frédéric Berthelot 04 Feb '13

04 Feb '13

Hi list, When working to get a tool wrapper Toolshed-ready, I have explored how tool dependencies installation works, especially the download_by_url feature. I have summarised my understanding on the Wiki (hope this is clear and accurate): <http://wiki.galaxyproject.org/ToolShedToolFeatures?action=diff&rev1=33&rev2…> The difference of behaviour when dealing with a Tar and a Zip file lies in the methods tar_extraction_directory() and zip_extraction_directory() (in [1]), which try to locate the deflated files: * zip_extraction_directory() counts the number of non- .zip “files” in the current directory. If more than one, the current path is returned ; if one, this “file” is assumed to be the deflated directory, and the full path to this directory is returned. The file_name variable (set to the name of the downloaded file) is not used. * tar_extraction_directory() which takes the name of the downloaded_file and removes the extension. If a subdirectory of that name exists, it is returned . Otherwise, if the full path to the downloaded file exists, the current path is returned. Otherwise, an exception is raised. This difference of behaviour can be very confusing. My wrapper local installations kept failing because for my tool, the deflated directory name did not match the tar.gz name. I was confused because I was using the bowtie wrapper [2] as an example, where it is not an issue. The obvious workaround is to use the target_filename attribute to have the downloaded archive name match the subdirectory name (which I have done, and it works perfectly now). But I was wondering if it would be a good idea to harmonize both methods behaviour? (P.S. As I am not very familiar yet with the Galaxy development process, I believe posting here is appropriate ; but I’d be happy to open an issue − on the Trello if I am not mistaken? − if needed. ) [1] <https://bitbucket.org/galaxy/galaxy-central/src/f49ce2c1883e/lib/galaxy/too…> [2] <http://toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/file/0c7e4eadfb…> Cheers, -- Jean-Frédéric Bonsai Bioinformatics group

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Re: [galaxy-dev] HTML output, hide "preview" text box?
by Jeremy Goecks 04 Feb '13

04 Feb '13

> My outputs section in the tool's xml file is: > > <outputs> > <data format="HTML" name="fred_report" label="generating FRED report..."/> > </outputs> You should set the output format to 'html' — all lower case. Galaxy has a list of known dataset types in datatypes.conf, and your output format should always match one of those in the file. Finally, please always include the mailing list in your reply so that emails are tracked and archived. Best, J.

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HTML output, hide "preview" text box?
by DePasse, Jay V 03 Feb '13

03 Feb '13

Hello, Hope this is an easy request: I've set up a tool that produces HTML output. All works great, but I was hoping that there's an easy way to remove the "preview" text box from the resulting History pane item (it currently shows the unrendered html tags)? Any help greatly appreciated! Thanks, -- Jay

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galaxy api documentation
by mark.rose＠syngenta.com 03 Feb '13

03 Feb '13

Hi All When is it anticipated that the documentation for the API will be available? 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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installing phylop
by Dinanath Sulakhe 03 Feb '13

03 Feb '13

I am trying to setup PhyloP in galaxy. In the add_scores.loc file it says we need the phyloP46way.primate.bw (BigWig) file. #hg19 /galaxy/data/hg19/misc/phyloP46way.primate.bw Is there a downloadable bigwig files somewhere for hg19 that I can use? >From the instructions on bigwig, it looks like we have to create a bigwig file from the wig files. Thanks, -Dina

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galaxy assumed linux shell
by Hagai Cohen 03 Feb '13

03 Feb '13

Hi, There are couple of Linux shells: bash, sh, zsh, csh. etc I would like to know if Galaxy is written to be supported on a specific one or it is written to support any linux shell? I'm asking this, because I want to add some features and I want to know what shell should I support? Or should write cross-shell code? In Dramaa runner, for example, it uses sh shell (inside drm_template inside drmaa.py), so any job that is run through this runner should support sh. Thanks, Hagai

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How to submit contribution to the Galaxy source code?
by Christos Kannas 02 Feb '13

02 Feb '13

Hi, We are developing on a local instance of Galaxy and I have made some modifications that I would like to share with the community. The modifications I've made are: 1. Modified objectstore to handle composite datasets containing subfolders. 2. Added csv datatype, consists of a class extending Tabular and a mako template to display data in a tabular format. So my question is how can I make these contributions available to the community? Should create a repository in Bitbucket and do a pull request? Or is there another way? 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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Can't specify workflow parameters for integer values
by Liisa Koski 01 Feb '13

01 Feb '13

Hello, I created a simple workflow with an input file and the 'Select first' tool. I wanted the value to be a parameter ${value}. I am able to save the workflow and see the little grey parameters box at the top of the workflow editor. When I try to run this workflow I get a yellow box at the top of the window stating the following: Problems were encountered when loading this workflow, likely due to tool version changes. Missing parameter values have been replaced with default. Please review the parameter values below. I do not however see an error in paster.log When I reopen the workflow in the editor I get a popup window saying 'Workflow loaded with changes' Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save. Step 2: Select first Value no longer valid for 'Select first', replaced with default I am running two instances of Galaxy (Jan. 11 distributuion) and this occurs in both of my instances. Will other workflows as well. But it appears to only occur for integer parameters...not text parameters. Any help would be much appreciated. Liisa

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Re: [galaxy-dev] File Upload doesn't generate any activity
by Dan Tenenbaum 01 Feb '13

01 Feb '13

On Fri, Feb 1, 2013 at 8:41 AM, Stephen Groenewold <sgroenewold(a)idtdna.com> wrote: > We’ve installed a local instance of Galaxy and are having trouble with the > first step of uploading files. The only thing that will currently upload is > text pasted into the URL/Text box. > > > > Any attempt to upload a file using the Browse File box not only fails, it > never even starts. It’s as if the Execute button is disabled. > > > > I’ve tried changing the ajax-upload parameter to “false” in > tools/data_source/upload.xml (as mentioned in a workaround posted to the > list by Daniel Blankenburg in Aug 2012). I’ve also tried using different > browsers (including Internet Explorer) and going the route of Adding Data > Libraries as Admin. None of those attempts have worked. > > > > Am I missing a configuration setup? Could there be permissions issues on the > Galaxy machine? > > This sounds like the same issue I've reported to this list, which Carl and others have been kind enough to look at. I think their look is still in progress but hopefully there will be some news about it soon. Here is that thread: http://dev.list.galaxyproject.org/error-uploading-file-with-fresh-installat… Dan > > Thanks. > > > > Steve > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/

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