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?


        

      

      

      

      

      
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