Re: [galaxy-dev] Galaxy code: data libraries

2013-12-02 Thread Misharl mon
Hi John, Thank you very much for your reply! I will try this, and inform you if it works correctly. Thank you again, Mish Date: Thu, 28 Nov 2013 15:06:47 -0600 Subject: Re: [galaxy-dev] Galaxy code: data libraries From: chil...@msi.umn.edu To: mish...@hotmail.com CC:

Re: [galaxy-dev] hmmer install

2013-12-02 Thread Peter Cock
On Mon, Dec 2, 2013 at 4:50 AM, Karen Miga khm...@soe.ucsc.edu wrote: Hi Greg, Thanks for the feedback. I cannot seem to find information for hmmdb.loc. When I look in the associated xml file it looks like it could be removed completely (does one need a precompiled HMM Database? I do not

Re: [galaxy-dev] Including descriptions etc in extended BLAST+ tabular output

2013-12-02 Thread Peter Cock
On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning wrote: Peter wrote: Great. I'll probably merge the c25 branch and push that to the Test Tool Shed next week (adding the descriptions as a new 25th column to the default extended tabular output). +1 The 24 column output will be replaced, right?

Re: [galaxy-dev] Including descriptions etc in extended BLAST+ tabular output

2013-12-02 Thread Nicola Soranzo
Il 2013-12-02 13:08 Peter Cock ha scritto: On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning wrote: Peter wrote: But, I would think we should offer the option to get all available result information. The multi-select checkboxes could serve that purpose. OK, so adding a pick-you-own columns

Re: [galaxy-dev] Including descriptions etc in extended BLAST+ tabular output

2013-12-02 Thread Jim Johnson
On 12/2/13, 7:03 AM, Nicola Soranzo wrote: Il 2013-12-02 13:08 Peter Cock ha scritto: On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning wrote: Peter wrote: But, I would think we should offer the option to get all available result information. The multi-select checkboxes could serve that

Re: [galaxy-dev] Including descriptions etc in extended BLAST+ tabular output

2013-12-02 Thread Peter Cock
On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi, On Fri, Nov 29, 2013 at 3:26 PM, Jim Johnson johns...@umn.edu wrote: Peter, It's good news that the description field is available in tabular format. That has been the primary reason for

[galaxy-dev] job_conf.xml output_size limit

2013-12-02 Thread Sarah Diehl
Hi everyone, in my job_conf.xml I defined the following limit limit type=output_size536870912000/limit Galaxy seems to correctly identify the number as 500 GB, since I got the error: Job output file grew too large (greater than 500.0 GB), please try different inputs or parameters The problem

[galaxy-dev] GCC2014 Training Day: Topic Nomination is now open

2013-12-02 Thread Dave Clements
Hello all, Training Day topics are nominated by you http://bit.ly/gcc2014tdnom, the Galaxy Community. Please take a minute to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see

Re: [galaxy-dev] Subclassing downloadable archive file for composite datatypes

2013-12-02 Thread John Chilton
Peter, I have pushed your patch along with a fix for the ext problem into galaxy-central. I don't think the fix will modifies the behavior in such a way that your implementation will be affected but let me know if I have broken something. Overall, this seems like a solid change to me - thanks

Re: [galaxy-dev] Subclassing downloadable archive file for composite datatypes

2013-12-02 Thread Peter Cock
On Mon, Dec 2, 2013 at 6:50 PM, John Chilton chil...@msi.umn.edu wrote: Peter, I have pushed your patch along with a fix for the ext problem into galaxy-central. I don't think the fix will modifies the behavior in such a way that your implementation will be affected but let me know if I

[galaxy-dev] survey

2013-12-02 Thread Philippe Moncuquet
Hi, I hope this is relevant to the dev list but if it is not please let me know. I was trying to estimate active users out of our registered users. I ended counting users that had a job during the last month. How would you guys do ? During this process I also wanted to see how we were doing in

[galaxy-dev] phyloviz: save visualization error

2013-12-02 Thread Karen Miga
Hello, I am trying to use phyloviz on the cloud/Galaxy cloudman. Unfortunately, I am unable to save the visualization using the save/disk icon on the right hand side of the banner. Any help would be appreciated. Karen ___ Please keep all

Re: [galaxy-dev] survey

2013-12-02 Thread Dave Clements
Hello Philip, all I'm working on a complementary effort that I was going to announce later this week, but maybe I'll just introduce it now. Something that came out of the GalaxyAdmins meetup in Oslo was a desire for some way for the community to describe the details of their Galaxy deployments