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 [email protected] Dr Shane Sturrock [email protected] Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand
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