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.gruen...@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 supp...@biomatters.com
>> 
>> 
>> Dr Shane Sturrock
>> shane.sturr...@biomatters.com
>> 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 supp...@biomatters.com

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

Attachment: smime.p7s
Description: S/MIME cryptographic signature

___________________________________________________________
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/

Reply via email to