Hi Bjoern, I've upgraded our machine and confirmed it now works fine. Thanks for that! Shane On 22/08/2013, at 5:17 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
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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-- 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