Hi Shane,

please find a new bismark version with an updated dependency on samtools
0.1.19 here:

http://toolshed.g2.bx.psu.edu/view/bgruening/bismark

Thanks for reporting that issue,
Bjoern

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 support@biomatters.com


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


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