[galaxy-dev] bwa setting metadata

Hi, I am running bwa using reference sacCer2. I have locally installed data for sacCer2 and the following line in builds.txt: sacCer2 S. cerevisiae June 2008 (sacCer2) This seems to work fine for other tools (e.g extracting genomic sequence). When I run bwa the job runs correctly but the d

[galaxy-dev] Toolshed fasta-section down?

Hi The fasta-manipulation section on toolshed seems to be down (http://toolshed.g2.bx.psu.edu/). Am I the only one experiencing this? IE just returns me a blank error page not found. FF returns me another unhelpful error: Server Error An error occurred. See the error logs for more

Re: [galaxy-dev] Workflow API (runtime modification of tool parameters)

Richard, We do have a very high level doc on the wiki describing the galaxy architecture in general, and api-specific documentation is under construction. http://wiki.g2.bx.psu.edu/Admin/Internals/Implementation%20Info http://wiki.g2.bx.psu.edu/Admin/API Specific to what you want to do with the

Re: [galaxy-dev] Configuring Toolsheds

Hi Zachary, On Dec 8, 2011, at 10:11 AM, Zachary Charlop-Powers wrote: > Greg, > > I thought I sent the e-mail below last night. Sorry. I reinstalled Galaxy > and ran into the same issue. Since I can modify my own tools and the > Toolsheds are not strictly necessary for what we are doing I am

[galaxy-dev] Excel upload problems

Hello! For our future galaxy users in Netherlands Bioinformatics Centre we'd like to support Excel uploads. We have our own excel to tabular CLI tool and I have been trying to get it working with galaxy. The tool itself is not the problem, but getting excel files uploaded is… We're running a l

[galaxy-dev] Cloudman and parameterized launching

Hi Guys, This is only sort of a Galaxy question, in the sense of "how did you guys do that so I can too" sort of way. I'm trying to clean up some code written by an undergrad for the GBrowse2 cloud machine, where he used less than secure methods of doing things. I gather from the page on Cloudma

Re: [galaxy-dev] FTP GALAXY

Hi We have set up galaxy in a production environment and our galaxy users can connect to the FTP and upload files. No worries. The settings in the universe file seem correct and are. ftp_upload_dir = /home/galaxy/galaxy-dist/database/ftp It creates the directory and uploads the file. But wh

[galaxy-dev] Send data to Galaxy from external websites.

Hi, I searched the docs and mailing list but could not figure out how to export data from my website directly to the *Main* public galaxy. My webserver creates a bed file and has meta information like build, genome etc. I would like to provide users with a button that allows them to directly send

Re: [galaxy-dev] FTP GALAXY

On Dec 7, 2011, at 10:19 PM, James Boocock wrote: > Hi > > We have set up galaxy in a production environment and our galaxy users can > connect to the FTP and upload files. No worries. > > The settings in the universe file seem correct and are. > > ftp_upload_dir = /home/galaxy/galaxy-dist/dat

Re: [galaxy-dev] Excel upload problems

Hello Siemen, You'll have to treat Excel files as a specific data type, and add support for that data type to Galaxy - see our wiki at http://wiki.g2.bx.psu.edu/Admin/Datatypes for details on how to add support for a new data type. You can implement the Excel class in such a way that nothing

Re: [galaxy-dev] Excel upload problems

Hey Siemen, A workaround i'm currently using consists of creating an Xls subclass of the Binary datatype class: In *galaxy-dist/lib/galaxy/datatypes/binary.py* add xls to * unsniffable_binary_formats* like this: *unsniffable_binary_formats = [ 'ab1', 'scf' , 'xls' ]* Also add the following clas

Re: [galaxy-dev] Excel upload problems

On Thu, Dec 8, 2011 at 4:29 PM, Joe Cruz wrote: > Hey Siemen, > > A workaround i'm currently using consists of creating an Xls > subclass of the Binary datatype class: That's not a workaround ;) - that's the correct approach, as per Greg's email. Not that I want to encourage people to use Excel

Re: [galaxy-dev] Excel upload problems

+1 I'd agree that calling it excel is suitably wry - because it doesn't IMHO. Please name the new binary datatype something other than xls because many (of my) tools create outputs with that extension and it's a subclass of tabular here - the .xls extension fools excel into loading them automagical

[galaxy-dev] January 2012 Galaxy Events: Dec 15 Deadline for Czech Republic Workshop

Hello all, The January Events email is going out a little early this month, mainly because of a *December 15 deadline for the Galaxy Developer Workshop in the Czech Republic *. There are Galaxy-related eve

Re: [galaxy-dev] Excel upload problems

> On Fri, Dec 9, 2011 at 3:35 AM, Peter Cock wrote: >> >> P.S. Why do you call your class XIs, surely Excel would be >> clearer? I've only just realised Xls is title case xls (as in the extension), I read it at the title case of xis (which made no sense). I still think using Excel as the class na

Re: [galaxy-dev] Cloudman and parameterized launching

Scott; The user passes in the AWS access and secret keys in the user-data box. This page has all the details about the YAML format CloudMan expects (in step 2 of the detailed steps): http://wiki.g2.bx.psu.edu/Admin/Cloud You can pick the passed in user-data up from any instance with this url: h