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
>>
>
>
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