[galaxy-user] Production environment

2012-02-10 Thread David Castillo
Hello, I've just installed Galaxy in my server in order to run it locally but there's a couple of tasks I haven't been able to complete, I hope somebody could advice me on how to accomplish them: I wanted to be able to have direct access to the contents stored in

Re: [galaxy-user] How to do BLAST on Galaxy sever?

2012-02-10 Thread Peter Cock
On Thu, Feb 9, 2012 at 9:57 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Peter, It looks to me like there are versions both, with the Tool Shed version having the more recent date stamp. But if those extra functions are not needed, then yes, you are correct, the version included in the

Re: [galaxy-user] Production environment

2012-02-10 Thread Greg Von Kuster
David, I can answer your first question, but will leave it to others to answer your second as I am less likely to answer it correctly. Regarding uploading files from your server, use the Upload files (to data libraries) from file system paths but do not copy into Galaxy's default file store.

Re: [galaxy-user] Production environment

2012-02-10 Thread Dannon Baker
On Feb 10, 2012, at 3:28 AM, David Castillo wrote: • I haven't been able to 'Edit' Workflows like in the public server, I have been able to create them, but once I try to edit them it just attempts to load the 'Workflow Editor' but it never does. How can I solve this? Do I have to

[galaxy-user] password reminder

2012-02-10 Thread c.sun
Dear sir or madam, I can not receive the password reminder. Could you please help me out? Thanks in advance! Best Chong ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server

Re: [galaxy-user] How to do BLAST on Galaxy sever?

2012-02-10 Thread Jennifer Jackson
David, I think we should go with Peter's advice. I had seen a date of April 2011 in the distribution for the tools I examined, but he knows these tools very well, and I could have easily missed the July 2011 date. Loading from the Tool Shed is not difficult, but perhaps unnecessary. So, for

Re: [galaxy-user] How to do BLAST on Galaxy sever?

2012-02-10 Thread Jennifer Jackson
David, I think we should go with Peter's advice. I had seen a date of April 2011 in the distribution for the tools I examined, but he knows these tools very well, and I could have easily missed the July 2011 date. Loading from the Tool Shed is not difficult, but perhaps unnecessary. So, for

[galaxy-user] Column Concatenation

2012-02-10 Thread La Chi
Hi , I am trying to fetch multiple column from a table here is my code for row in result_set:         db += [(row ['chr'],str(row[ 'user_id' ]), False),] i want to concatenate 'start' column and 'end' column with this output , how can i do that

[galaxy-user] Solution for: Error running cuffdiff. Error: cannot open reference GTF file CONDITION, CONTROL for reading

2012-02-10 Thread Carlos Borroto
Hi, I ran into this error running cuffdiff. I had a hard time debugging this user error, so I though it would be nice to share the solution. This was in a local instance, but I don't see why it wouldn't happen in Galaxy Main under the same circumstances. Tool execution generated the following