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



On 26 November 2014 at 13:49, Anna Terry <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

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