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 <[email protected]> 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 <[email protected]> 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
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>
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