galaxy-dev November 2009

galaxy-dev@lists.galaxyproject.org

26 participants
233 discussions

Re: [galaxy-dev] Current Logged in User
by Greg Von Kuster 03 Nov '09

03 Nov '09

Hello Raghav, "trans" is the object defined by the UniverseWebTransaction class in ~/lib/galaxy/__init__.py, and is available in any of the mako templates and controller methods, and many other methods as well. In the future, please send questions like this to the galaxy- dev(a)bx.psu.edu mail list. Thanks very much, On Nov 3, 2009, at 5:51 AM, Raghav Bhatnagar wrote: > Hi Greg > I have a very basic question but somehow I could not figure it out. > I am trying to get the details of current logged in user. I can get > the workflows made by the user by mapping it from galaxy_user and > storedworkflow table from universe.sqlite database. But I am having > problem fetching the current logged in user. > > Now I saw the python scripts and almost every file calls the > function trans.get_user(). > I could not figure out where the function is defined. > Please help me getting the id of the current logged in user. > > Regards, > > -- > Raghav Bhatnagar > Graduate Student (CS) > Viterbi School of Engineering > University of Southern California Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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Dynamic GUI for genome-browser custom tracks (another long email)
by Assaf Gordon 02 Nov '09

02 Nov '09

Hello, I'd like to suggest a feature that would make uploading custom tracks from Galaxy to the UCSC genome browser friendlier (IMHO). I don't have the code for it, this is just a suggestion, open for discussion. The way it works now - there are two options to upload custom tracks: 1. click on "Main" link - send the file as is to UCSC's genome browser. Track attributes (color, name, visibility, score, etc) are not sent. Track name is "User Track". If another track is uploaded - it overrides the previously uploaded track. 2. Run the "Build Custom Track" in the "Graph/Display Data" category. This allows setting track options, but it duplicates the existing file, and the options as statically stored in the file - they can't be changed, and the file can't be further processed (unless one removes the custom track line). My suggestion has four parts: Part 1 ------ Each viewable file (BED, intervals, PSL, Wiggle, BedGraph and in the future: SAM/BAM, bigWig, bigBed) will have another 'button' called "custom track attributes" (or a shorter, better name). Clicking on this button will show the user a page in which the user can set the common custom track options. See a mock-up here: http://cancan.cshl.edu/labmembers/gordon/custom_tracks_ui/genome_browser_cu… This page is purely client side - code is javascript. The "output" of this page is just one text line - the custom track attributes line. Part 2 ------ A new database table in galaxy will store the "custom track line" for each eligible dataset. When the user clicks on the above mentioned button, the line is read from the table. When the user clicks "OK" on the above page, the line is saved back to galaxy. Part 3 ------ A new method in the datasets controller will "inject" the dataset's custom line before sending the file's content. For example, if my dataset is a BED file, and contains: chr1 100 3000 chr2 200 3000 And my custom-track-line for this dataset is: name="Hello World" visibility=4 color=255,0,255 The new method will first send the custom-track-line, followed by the actual dataset content: track name="Hello World" visibility=4 color=255,0,255 chr1 100 3000 chr2 200 3000 This method will require just a couple of tricks: adding the "track" keyword at the beginning of the line, and adding the "type" keyword if this is not a standard BED file (e.g. for Wiggle/PSL/BedGraph) Part 4 ------- When click on the "main" button (to display the track in the genome browser), Galaxy will send this new method to the UCSC genome browser, instead of the raw data file. Outcome ------- Uploading custom tracks (with more attributes) will be much easier - no need to run an extra tool. One could them change display options are 'reload' a track (or by using the genome browser's reload button). No need for duplicated data files in galaxy, and tracks can be further processed, filtered, etc (if the custom-track-line) is copied from one dataset to another like other metadata. Further improvement ------------------- When (if?) galaxy supports large binary files (BAM, bigWig, bigBed), it could take advantage of the genome browers's 'bigDataUrl' feature: The new method (in part 3) doesn't need to transmit the entire dataset content into the genome browser. Instead can return the custom track line, and add the 'bigDataUrl' key, with the URL pointing to the real "display" method of the dataset. Something like: track name="Hello World" type=bigBed visibility=3 color=255,255,0 bigDataUrl=http://main.g2.bx.psu.edu/datasets/f8bca8dcf7f5c1d8/display/?sho… And then binary tracks are uploaded almost immediately, and the genome browser will query galaxy just for the parts of the file that are needed. As always, comments are welcomed. -gordon.

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Latest download from repository
by Dijk, F van 02 Nov '09

02 Nov '09

Hi, I have two questions to ask, firstly: We've experienced some errors with Galaxy lately so we decided to download the latest copy from your repository. After installing it, it seems like some tools like "mapping with Bowtie and BWA" are missing. When running run.sh it looks like they aren't loading properly. Yesterday we did also download from these repositories and we didn't experience these errors, so do you know what the problem can be? Second: What version of python do you use for Galaxy, because the older python versions we use seem to give some problems. I hope to hear from you soon. Sincerely Freerk van Dijk De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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galaxy-dev November 2009