Re: [galaxy-dev] Programmatically deleting data sets from data libraries?

2012-09-05 Thread Sajoscha Sauer
Hi Dan, I had a similar problem just yesterday. I couldn't enter the 'Data library' via the API anymore because one of the dataset files wasn't available anymore (or actually it was, but someone had a space in the filename...). So, to be able to enter the 'Data library' again, I had to remove

Re: [galaxy-dev] Toolsheds and job runners

2012-09-05 Thread Paul-Michael Agapow
Thanks Greg, In case you are not aware of it, the Galaxy tool shed wiki explains the tool shed: http://wiki.g2.bx.psu.edu/Tool%20Shed I am aware, thanks, although I won't exclude the possibility that I've misunderstood something ... I've inherited a galaxy setup from someone (details: a

[galaxy-dev] fetch sequences

2012-09-05 Thread Deepthi Theresa
Hi all, I want to fetch sequences from a file(in interval format) using custom genome build(using built-in index). How can I do that? I tried fetch sequences in the menu. But I could not find option for a custom genome. Thanks, Deeps

Re: [galaxy-dev] fetch sequences

2012-09-05 Thread Jennifer Jackson
Hello Deeps, On the tool form for Extract Genomic DNA a custom genome can be used once the genome is loaded into your history as a fasta file. Instructions for how to load/prepare a custom genome, including a prep screencast and troubleshooting tips, are in this wiki:

Re: [galaxy-dev] Would like to Post to Galaxy List

2012-09-05 Thread Jennifer Jackson
Hi Gloria, Here are the instructions for subscribing to Galaxy's lists: http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing And here is a bit more detail about where to post, based on the question type. In general, if you have a question about cloud issues, this list

Re: [galaxy-dev] [galaxy-user] git mirror

2012-09-05 Thread Shantanu Pavgi
On Sep 5, 2012, at 4:55 AM, Luca Pireddu wrote: On 09/05/2012 01:30 AM, Peter Cock wrote: On Tue, Sep 4, 2012 at 5:57 PM, Luca Pireddu pire...@crs4.it wrote: Hello list. A simple question: is there a git mirror of the Galaxy repositories? If not, what do git users here do to work with