What is really weird is when running the bowtie2 tool, before it quits, I
can see samtools come up in top

On 26 November 2014 at 15:55, Anna Terry <iseegl...@googlemail.com> wrote:

> So I actually still have a problem,
> (I guess the setting was still there somewhere from the bash_profile)
>
> Anyway, I am also getting the problem with samtools filter sam or bam
>
> 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
>
> I have tried also what you said, linking the samtools binary to default, but 
> still the same problem.
>
> Any other ideas?
>
>
>
> On 26 November 2014 at 14:01, Anna Terry <iseegl...@googlemail.com> wrote:
>
>> Great, I've done it and it works.
>>
>> galaxy-dist/tools/samtools/default
>> cd galaxy-dist/tools/samtools/default/
>> cp -rs ~/galaxy-dist/tools/samtools/0.1.19/* .
>>
>> Thanks Bjoern and Eric
>>
>>
>> On 26 November 2014 at 13:54, Eric Kuyt <eric.ku...@wur.nl> wrote:
>>
>>> Bjoerns comment was the right one, samtools isn't automatically
>>> installed as a dependency somehow.
>>>
>>> so the best option is to install samtools
>>> https://toolshed.g2.bx.psu.edu/view/devteam/package_samtools_0_1_19
>>>
>>> and link the installed binary to ~/tool_deps/samtools/0.19/iuc/2828727744/
>>> to ~/tool_deps/samtools/default
>>>
>>> Eric
>>>
>>>
>>> On 26 November 2014 at 14:44, Anna Terry <iseegl...@googlemail.com>
>>> wrote:
>>>
>>>> Here is the contents of the log file:
>>>>
>>>> Successfully downloaded from url:
>>>> http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.1.0-linux-x86_64.tgz
>>>>
>>>>
>>>> On 26 November 2014 at 13:26, Eric Kuyt <eric.ku...@wur.nl<mailto:
>>>> eric.ku...@wur.nl>> wrote:
>>>> Hi Anna,
>>>>
>>>> Setting your own path variables shouldn't be necessary for toolshed
>>>> tools, so probably something is wrong with the installation. could you post
>>>> your
>>>>
>>>>
>>>> tooldependencies/bowtie2/2.1.0/devteam/package_bowtie2_2_1_0/017a00c265f1/INSTALLATION.log
>>>>
>>>> file?
>>>>
>>>> On 26 November 2014 at 13:49, Anna Terry <iseegl...@googlemail.com
>>>> <mailto:iseegl...@googlemail.com>> wrote:
>>>> Hi,
>>>> I installed bowtie2 from the toolshed, but get the following error when
>>>> I run it:
>>>>
>>>>
>>>> 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
>>>>
>>>> I'm not sure why this won't work?
>>>> samtools is a dependency for the bowtie2 tool and is installed, but
>>>> cannot seem to find it.
>>>> There must me something slightly wrong on my server as I can't see
>>>> loads of errors like this on this mailing list.
>>>>
>>>> I have added the path from the samtools env file to .bash_profile for
>>>> galaxy and this allows this tool to run,  but is not the correct solution,
>>>> as doesn't work when versions change.
>>>>
>>>> Could you let me know where I'm going wrong
>>>> Thanks
>>>> Anna
>>>>
>>>>
>>>>
>>>> --
>>>> 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<mailto:eric.ku...@wur.nl>
>>>> Web: http://www.cvi.wur.nl
>>>>
>>>>
>>>
>>>
>>> --
>>> 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
>>>
>>
>>
>
___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to