Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Nicola Soranzo
Il giorno mar, 19/03/2013 alle 15.20 -0400, Raj Ayyampalayam ha scritto: One of the first few tools I tested was the ncbi makebkastdb tool. When I try to run it the history for that particular job is immediately shown as follows: 0: (unnamed dataset) Failed to retrieve dataset

Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Peter Cock
On Wed, Mar 20, 2013 at 10:08 AM, Nicola Soranzo sora...@crs4.it wrote: Il giorno mar, 19/03/2013 alle 15.20 -0400, Raj Ayyampalayam ha scritto: One of the first few tools I tested was the ncbi makebkastdb tool. When I try to run it the history for that particular job is immediately shown as

Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Nicola Soranzo
Il giorno mer, 20/03/2013 alle 12.41 +, Peter Cock ha scritto: On Wed, Mar 20, 2013 at 10:08 AM, Nicola Soranzo sora...@crs4.it wrote: Il giorno mar, 19/03/2013 alle 15.20 -0400, Raj Ayyampalayam ha scritto: One of the first few tools I tested was the ncbi makebkastdb tool. When I

Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Peter Cock
On Wed, Mar 20, 2013 at 1:55 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Mar 20, 2013 at 1:52 PM, Nicola Soranzo sora...@crs4.it wrote: Il giorno mer, 20/03/2013 alle 12.41 +, Peter Cock ha scritto: The patch just removes the MetadataElement call - is that wise? Hi Peter, my

Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Raj Ayyampalayam
Hi Guys, Thanks for the quick response. I installed the latest blast datatypes from the toolshed and that fixed the issue. Peter, can you also fix the $outfile.extra_files_path to $outfile.files_path on line 5 in the makedb wrapper xml file. Thanks, -Raj On Wednesday, March 20, 2013

Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Peter Cock
On Wed, Mar 20, 2013 at 3:43 PM, Raj Ayyampalayam ra...@uga.edu wrote: Hi Guys, Thanks for the quick response. I installed the latest blast datatypes from the toolshed and that fixed the issue. Great - thanks for letting us know so promptly. Peter, can you also fix the

Re: [galaxy-dev] Problem running ncbi_makeblastdb as real user in cluster

2013-03-20 Thread Peter Cock
On Wed, Mar 20, 2013 at 3:47 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Mar 20, 2013 at 3:43 PM, Raj Ayyampalayam ra...@uga.edu wrote: Hi Guys, Thanks for the quick response. I installed the latest blast datatypes from the toolshed and that fixed the issue. Great - thanks for