Jennifer -

Yes, I installed Galaxy that same day with:

   1 % hg clone https://bitbucket.org/galaxy/galaxy-dist/
   2 % cd galaxy-dist
   3 % hg update stable

Then I searched for bwa_wrappers in the toolshed (there were only two matches) and chose the devteam one.

What steps should I go through or log files should I submit to help track the problem down?

Thanks -

Joshua


On Mon, Sep 30, 2013 at 9:36 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Joshua,

Just to double check, you are running the latest stable distribution?

There are a few different BWA wrappers in the tool shed, maybe you are using a different one than previously? Using a custom reference genome from the history with bwa is possible with the wrapper with the owner "devteam" (assuming Galaxy is installed where there are suitable resources - same as command line bwa).

If you want to try again and report back any ongoing issues, please use the galaxy-dev@bx.psu.edu mailing list to reach the development community (drop galaxy-user@bx.psu.edu from the to or cc).

Thanks,
Jen
Galaxy team



On 9/27/13 7:37 PM, Joshua Orvis wrote:
I installed a new copy of galaxy today and then added the bwa_wrappers tool.  After I upload my reference genome and left/right reads I get output like this each time I try to run bwa for illumina:

The alignment failed.
Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwt_restore_bwt] fail to open file '/seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat.bwt'. Abort!
/bin/sh: line 1: 11607 Aborted                 bwa aln -t 4 -I /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_4.dat /seq/gscidA/www/gscid_devel/htdocs/galaxy-dist/database/files/000/dataset_2.dat > /tmp/tmpMuj4l2/tmpUIdxXT

          
If I manually do the 'bwa index' command on dataset_4.dat it works but in the past this seemed to happen automatically.  Any clue what's going on here?


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

-- 
Jennifer Hillman-Jackson
http://galaxyproject.org