Hi Bjoern,
We could default to using sorted BAM files from Bismark as that is Ok with 
methylkit which we use for our downstream analysis. On the other hand we still 
need the unsorted BAM files for methylation extractor which we use for 
visualisation.
Thanks for the reply and I'll wait for the workaround.
Cheers,Cristian

> Date: Mon, 8 Jun 2015 11:22:44 +0200
> From: bjoern.gruen...@gmail.com
> To: tuto...@hotmail.com; galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Bismark doesn't end and blocks the server
> 
> Hi,
> 
> I think this is a general problem you encountered here with unsorted BAM
> files. We can reproduce it locally. Will let you know if I find a
> workaround.
> 
> Cheers,
> Bjoer
> 
> Am 05.06.2015 um 14:23 schrieb C. Ch.:
> > 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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