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
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