I've had a bit of a time trying to get Bismark working on our Galaxy instance.  
The install doesn't work because of the dependency on samtools 0.1.18 but in 
fact it requires samtools 0.1.19.  I have a build of that installed as standard 
on our system so putting a symlink to that in the place of the samtools built 
for the bismark wrapper makes it work - I was seeing issues where the BAM file 
wasn't created and noticed in Bjoern's readme.rst that said it required 
samtools 0.1.19 or later.

Shane

--
For urgent cases, contact supp...@biomatters.com

Dr Shane Sturrock
shane.sturr...@biomatters.com
Senior Scientist
Tel: +64 (0) 9 379 5064
76 Anzac Ave
Auckland
New Zealand

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