November 2011 - galaxy-dev - lists.galaxyproject.org

Tools appearing without inputs in workflow editor
by Steven Platt 21 Nov '11

21 Nov '11

A colleague of mine posted this on the Users list ... 4 days later and no replies! I'm hoping that one of the Devs can shed a bit of light ------------------------------------------------------------------------ --------------------------------------------------- A peculiar bug, presented for your input: A colleague has built a few tools and is trying to incorporate them into a workflow. However: 1. When he creates an new empty workflow, edits it and adds the tools, they appear without inputs (i.e. the icons/boxes on the diagram have no input "sockets") 2. When he tries to save a history using these tools as a workflow, a error results in which Galaxy complains about an unrecognised name, being one of the tool inputs. Depending on which tool he includes in the workflow, the missing name occurs in whichever tool is earlier in the workflow. (Traceback available on request) Puzzling. And even more puzzling when I tried to debug this: 1. Other tools (not written by him) behave in the workflows as expected. 2. Pulling a copy of his config file across to my own instance of Galaxy and creating a dummy tool to house it, it worked perfectly 3. We're running the same version of Galaxy, albeit different versions of Python (2.5 vs 2.6.4) 4. The tools work fine in normal analysis mode. 5. Line-ending unix, XML seems to parse fine. I'm stymied here and unsure what to look at next. Ideas? ------------------------------------------------------------------------ --------------------------------------------------- Thanks Steve Dr Steven Platt Bioinformatician Health Protection Agency Microbiology Services Division London www.hpa.org.uk/bioinformatics ----------------------------------------- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk **************************************************************************

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bam to ucsc
by Ivan Merelli 21 Nov '11

21 Nov '11

Hi, I'm experiencing an error while trying to upload bam files from my local instance of galaxy to ucsc. In particular the bam tracks appear in the ucsc genome browser, but instead of data I got this error: End of file reading 1 bytes (got 0) I searched the mailing list, but the only hint I get is in the following mail, which however does not provide a solution for the problem, because I don't know how to enable the byterange (and whatelse) support for my server (in apache?). https://lists.soe.ucsc.edu/pipermail/genome/2011-July/026420.html Any ideas of what I should do? Maybe it can be helpful to provide a hint in the apache configuration howto. I.

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Grooming Error when linking bam files instead of copying into galaxy
by Chorny, Ilya 19 Nov '11

19 Nov '11

The uploaded files need grooming, so change your Copy data into Galaxy? selection to be Copy files into Galaxy instead of Link to files without copying into Galaxy so grooming can be performed. Thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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November 18, 2011 Galaxy Development News Brief
by Jennifer Jackson 18 Nov '11

18 Nov '11

November 18, 2011 Galaxy Development News Brief This release http://galaxyproject.org/wiki/News%20Briefs/2011_11_18 Release history http://galaxyproject.org/wiki/News%20Briefs Source http://getgalaxy.org Support http://galaxyproject.org/wiki/Support new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r b258de1e6cea Highlights GCC2012 is Scheduled! Galaxy tool sheds enabling sharing of workflows & tools New wrappers, new tool upgrades: Python, FASTQC, Picard, TopHat Direct Galaxy link to IGV Plus new Trackster features, UI and Source updates, Bug fixes All News & Events GCC 2012 is Scheduled! Upcoming Workshops and Presentations What's New Tool Shed: Enabling Workflow Sharing Using Tool Sheds Python Support Updated & Improved Tools Galaxy Track Browser (Trackster) Workflows User Interface (UI) External Display Applications Source Bug Fixes Thanks for using Galaxy!

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Re: [galaxy-dev] Problem with the Galaxy tool shed
by Greg Von Kuster 18 Nov '11

18 Nov '11

Hi Marcel, This should now be working - sorry about the delay on this - a lot of enhancements came with it. Thanks for your patience on this one! Greg On Nov 16, 2011, at 12:19 PM, Marcel Schumann wrote: > Hi Greg, > > yes, I tried to change the synopsis. > Now I tried it again and noticed that the tool shed displays an error message; I had just overlooked it previously, sorry for that. The error message is: > > "You are not the owner of this repository, so you cannot manage it." > > Well, I'm not sure why I'm not the owner of my repository, but perhaps you can find out ... ;-) > > > Cheers, > Marcel > > > On 11/16/11 5:32 PM, Greg Von Kuster wrote: >> Hi Marcel, >> >> >> On Nov 15, 2011, at 5:06 PM, Marcel Schumann wrote: >> >>> Hi Greg, >>> >>> wonderful, thanks a lot! >>> I actually had a look at the Galaxy tool shed a few hours ago, saw the few http-upload option and used it. It worked well, no problems there. >>> >>> But there are indeed two other small issues that I encountered after this: >>> -- Changing the tool-suite synopsis does not work anymore. I tried to change it in order to reflect the new version number, but after saving the changes, the page still shows the old version-number (i.e. the old synopsis). >> >> I am not able to reproduce this problem, assuming you changed the values in either the name, synopsis or detailed description fields on the "Manage repository" page in the tool shed like the screen capture here. Can you clarify that this is what you are trying to do? >> >> >> >> >> >> >> >>> -- Selecting an old repository revision and then using "Browse or delete files" will result in the list of files that are in the current revision of the repository. However, downloading works correctly; that is, if you select an old revision, you will really download the old version ... >> >> This is by design. Although you can preview tools, inspect tool metadata, data types, etc for older repository revisions, you can browse files contents and delete selected files only within the repository tip. I've made this more clear by changing the "Browse or delete repository files" to now be "Browse or delete repository tip files". >> >> The intent here is to make it easy to maintain the latest revision of the repository within the tool shed UI by enabling you to upload new files to the repository tip or delete selected files from the repository tip. This assumes you are not making changes to old versions of your tools and wanting to make them available in the tool shed. >> >> In order to push updates of old versions of your tools to the tool shed, you'll have to create a different tool shed repository for each version of your tools. >> >> >>> >>> >>> Thanks& best regards, >>> Marcel >>> >> >> Greg Von Kuster >> Galaxy Development Team >> greg(a)bx.psu.edu >> >> >> > > > -- > Marcel Schumann > > University of Tuebingen > Wilhelm Schickard Institute for Computer Science > Division for Applied Bioinformatics > Room C313, Sand 14, D-72076 Tuebingen > > phone: +49 (0)7071-29 70437 > fax: +49 (0)7071-29 5152 > email: schumann(a)informatik.uni-tuebingen.de Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

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error in downloading bai files using shared history link
by Shantanu Pavgi 18 Nov '11

18 Nov '11

Hi, We are getting following error when a user tries to download bam index file (bai) files using a shared history link of following pattern - ' https://galaxy.mydomain/u/user1/h/awesome-analysis '. We are using external authentication and latest galaxy-dist code in our set up. {{{ Error Traceback: View as: Interactive | Text | XML (full) ⇝ TypeError: get_metadata_file() got an unexpected keyword argument 'username' URL: http://galaxy.mydomain/dataset/get_metadata_file?username=user1&metadata_na… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:111 in __call__ view >> return self.app( environ, start_response ) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view >> body = method( trans, **kwargs ) TypeError: get_metadata_file() got an unexpected keyword argument 'username' }}} However, if the user imports this history then bai file download works fine. Is this a known issue or some problem with our set up? Anyone else experienced similar issues? -- Thanks, Shantanu.

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Delete toolshed repository
by Chorny, Ilya 18 Nov '11

18 Nov '11

I want to delete a test repository I created on http://toolshed.g2.bx.psu.edu/repository?webapp=community. Is that possible? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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Newbie question for toolshed development
by Aaron Quinlan 18 Nov '11

18 Nov '11

Hi Greg, I am in the process of trying to develop a set of Galaxy wrappers for the tools in my bedtools suite. I have read the Toolshed wiki, but I am still struggling with some very basic questions that I hope you can help me with. 1. How should a tarball repository be structured for the toolshed? For example, bedtools currently includes a Makefile plus a src/ directory and sub-directories for each tool. The compiled objects go to obj/ and the binaries to bin/. By reading the wiki I gather that I also need to add a new directory that contains an XML wrapper for each tool. Is that correct? Is there a specific name for said directory that is expected by the Toolshed? 2. Do you have an example repository that has a similar structure to what is described in #1? This would be very helpful as a means to follow the lead of something that already works. I apologize if answers to these questions are made abundantly clear somewhere yet I have somehow missed it. Best, Aaron

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Name your own tool's output?
by Timothy Wu 18 Nov '11

18 Nov '11

Hi, I thought I had already asked this question a while ago, but I can't find it so I guess I haven't. When porting my own tool, is there anyway to customize the name of the output? Timothy

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Dynamic tool configuration
by Rodriguez, Aaron (NIH/NCI) [C] 17 Nov '11

17 Nov '11

Greetings, I'm looking to add a tool that works with a custom datatype that would dynamically generate input parameter options based on the dataset metadata. For example, A dataset of type foo contains metadata as follows: descfields = ['label','description'] quantfields = ['qualityscore','othernumericvalue'] These values are parsed directly out of the dataset and stored into the metadata via the foo datatype class. However the number of values within the list could vary among datasets of type foo. Now I'd like to configure a tool that generates input parameter for each of the descfields values in the list as well as for each of the quantfields values in its list. I understand that this may be outside of the scope of the current tool syntax but if anyone could provide some direction to how tools can be made more 'dynamic' using their metadata it would be greatly appreciated. One idea was to dynamically generate the <tool>.xml and dynamically loading it upon request. But not sure if this would integrate well. Thanks for your feedback! -AR

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