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 <[email protected]> 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 [email protected] >> >> >> Dr Shane Sturrock >> [email protected] >> Senior Scientist >> Tel: +64 (0) 9 379 5064 >> 76 Anzac Ave >> Auckland >> New Zealand >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > > > -- 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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