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.