The problem is that bowtie and Galaxy (can) use a different samtools
version. Galaxy needs samtools to create metadata for BAM files, so this
process is actually running ofter bowtie has finished.
You need a samtools version globally accessible for Galaxy. Make sure you
have smatools in your $PATH and than restart Galaxy.

Cheers,
Bjoern

2014-11-26 17:14 GMT+01:00 Anna Terry <iseegl...@googlemail.com>:

> I just tried still the same problem.
> I ran bowtie2 to test, again I saw samtools come up on top, but same error:
>
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, 
> in queue_job
>     job_wrapper.finish( stdout, stderr, exit_code )
>   File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in 
> finish
>     dataset.datatype.set_meta( dataset, overwrite=False )  # call 
> datatype.set_meta directly for the initial set_meta call during dataset 
> creation
>   File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, 
> in set_meta
>     raise Exception, "Error Setting BAM Metadata: %s" % stderr
> Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
>
>
>
> On 26 November 2014 at 16:01, Eric Kuyt <eric.ku...@wur.nl> wrote:
>
>> ​Could you try going to Admin -> Manage Installed tool shed repositories
>>
>> uninstall -> reinstall ​package_samtools_0_1_18
>>
>>
>> On 26 November 2014 at 16:55, Anna Terry <iseegl...@googlemail.com>
>> wrote:
>>
>>> yway, I am also getting the problem with samtools filter sam or bam
>>
>>
>>
>>
>>
>> --
>> Central Veterinary Institute of Wageningen UR (CVI)
>> Department of Infection Biology
>> PO box 65, 8200 AB Lelystad, NL
>> Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad
>>
>> Tel:  +31-(0)320-293391
>> Fax: +31-(0)320-238153
>> E-mail: eric.ku...@wur.nl
>> Web: http://www.cvi.wur.nl
>>
>
>
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