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
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