Hi all,
I have a clean local install of galaxy from git (commit: 
40b69cb948eed2cece82a32dfc5c6116414ab97c).I've installed bismark and I get an 
error message (see below) if I do not choose the 'sort' option.I have the 
impression that this might be related more to galaxy than to bismark itself. 
The result is that the server gets blocked and the only solution is to restart 
galaxy.
Any help is appreciated!Cristian
The error message:galaxy.datatypes.metadata DEBUG 2015-06-05 11:14:12,514 
setting metadata externally failed for HistoryDatasetAssociation 1305: External 
set_meta() not called[bam_index_core] the alignment is not sorted 
(HWI-ST278R:398:C1WUTACXX:3:1101:9378:2574): 2-th chr > 1-th 
chr[bam_index_build2] fail to index the BAM file.                               
         
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