Jennifer -

Yes, I installed Galaxy that same day with:

   1 
<http://wiki.galaxyproject.org/Admin/Get%20Galaxy#CA-6e8244969be36356bce6775f270761066e912e0d_1>
% hg clone https://bitbucket.org/galaxy/galaxy-dist/   2
<http://wiki.galaxyproject.org/Admin/Get%20Galaxy#CA-6e8244969be36356bce6775f270761066e912e0d_2>
% cd galaxy-dist   3
<http://wiki.galaxyproject.org/Admin/Get%20Galaxy#CA-6e8244969be36356bce6775f270761066e912e0d_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 <j...@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-...@bx.psu.edu mailing list to reach the development community
> (drop galaxy-u...@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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> --
> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>
>
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