[galaxy-dev] Apologies

Dear List, Apologies for that last email. It seems my gmail account has somehow been compromised Please don't click on the link. Ira ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your su

[galaxy-dev] Weird VDF format header

Hi,While technically not a Galaxy (Dev) question, but I am running into a non-standard VCF header in the GATK UnifiedGenotyper output.I see##FORMAT= ##INFO= ##INFO= Where Number=G and Number=A which does not pass the VCF Validator filter...Anyone know what is going on here? I had to change it to ac

Re: [galaxy-dev] Setting the output label based on input parameters?

We are also "feeling the hurt" of not being able to carry the input dataset names through a complex workflow. We are also very interested in a solution similar to what Dave Walton has proposed,. Dave, would it be possible to receive a copy of your modified code? Does it work when there are mu

Re: [galaxy-dev] Upload file local option no longer appears

Hi Jim, Admin only actions are accessed from under the Admin panel. Can you check that you are accessing the Library from under the Admin interface and not from under Shared Data? Thanks for using Galaxy, Dan On Feb 27, 2012, at 12:24 PM, James Vincent wrote: > Hello, > > I have been uplo

Re: [galaxy-dev] Trouble linking to/displaying at local Genome Browser

Hi Josh, Correct, to get the display functionality to work, your first two steps are sufficient. The other steps are only needed if you want to allow users to use your local mirror as a data source inside of Galaxy. If you don't want users to be able to use your local mirror as a data source,

[galaxy-dev] Upload file local option no longer appears

Hello, I have been upload files to data libraries using the local file option to give a list of system file paths. Upon restarting galaxy (because of server reboot) I no longer have that option. The universe file has not changed and contains this, as it always has: # Add an option to the library

Re: [galaxy-dev] Trouble linking to/displaying at local Genome Browser

One more thing while I'm at it. For clarification would only the first two steps I listed be sufficient to get the "display at" link in Galaxy? If so what is the benefit of the other steps (other than having an actual link to your local genome browser mirror in Galaxy)? There's nothing that ties my

Re: [galaxy-dev] Trouble linking to/displaying at local Genome Browser

Hi Dan, Good catch sir! Genius! It is working now. The spacing was exactly the same to the eye in vi for all the entries, but once I did a 'set list' in vi to display formatting characters I saw that 'main' had the tab ^I characters but my 'internalgb' entry didn't. This must have happened because

Re: [galaxy-dev] GATK metadata problems

Hi Curt, This is an annoyance when trying to use these tools interactively, but running or designing a workflow in the editor should work just fine. The issue is that for Galaxy the BAM index is technically considered an optional metadata attribute, but it is required for GATK. I've removed the

Re: [galaxy-dev] Trouble linking to/displaying at local Genome Browser

Hi Josh, It sounds like you are really close to getting this to work. My first guess would be that there is an issue with the modified ucsc_build_sites.txt file. Can you check that the line you copied is tab delimited and not space delimited? Thanks for using Galaxy, Dan On Feb 27, 2012, at

[galaxy-dev] Trouble linking to/displaying at local Genome Browser

Hello all, I am having some trouble getting a "display at" link to my local UCSC Genome Browser mirror to show up under my Galaxy jobs for viewing, although I can get the link to the online UCSC GB to display. I followed the suggestions in the following thread but it has yielded no results yet: ht

[galaxy-dev] Data not uploading in Local instance

Hi Luciano, I am going to forward you question over the to galaxy-...@bx.psu.edu mailing list where the development community will see and provide feedback to your question: http://wiki.g2.bx.psu.edu/Support#Mailing_Lists Best, Jen Galaxy team On 2/26/12 3:19 PM, Luciano Cosme wrote: I h

[galaxy-dev] Upload file script fails with OSError: [Errno 1]

Hello, I would like to report on a Galaxy issue and the my proposed solution for it, hopefully it will be helpful to other Galaxy users that encounter [are encountering] the same problem. I tried to upload to my local Galaxy a file that I has been transferred by a FTP client. Then, when Galaxy

[galaxy-dev] can the sample tracking system transfer (copy) data to a dataset library not in private Galaxy server data directory tree and then just link files?

Dear all, Is there a way with the Galaxy sample tracking system to have the dataset transfer feature copy data to a dataset library outside the private Galaxy server data directory tree and then the dataset library just link (like you can do with upload files feature when managing data libraries)?

Re: [galaxy-dev] universe_wsgi.ini

Hi Daniel, I have to admit it took me some time and a lot of trial and error to figure out how the .loc files work :) I'm glad it works for you now. I'm not fully sure about what exactly you want to do but here is what I think could be of help: If your Galaxy runs on the same machine your fi