great, thanks

On 26 November 2014 at 16:39, bjoern.gruen...@googlemail.com <
bjoern.gruen...@gmail.com> wrote:

> I would use .bashrc. You can also try to symlib the default dir to the
> actual /bin directory. Maybe this works for you.
>
> 2014-11-26 17:36 GMT+01:00 Anna Terry <iseegl...@googlemail.com>:
>
>> is bash_profile the best place for this, or is somewhere else better?
>>
>> Cheers
>> Anna
>>
>> On 26 November 2014 at 16:29, bjoern.gruen...@googlemail.com <
>> bjoern.gruen...@gmail.com> wrote:
>>
>>> 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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>>>
>>>
>>
>
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