On Mon, Feb 23, 2015 at 2:13 PM, Michael Thon <mike.t...@gmail.com> wrote:
> I figured that galaxy must be finding a samtools v1.1 even though the tool
> was not installed, according to the admin page. I uninstalled the samtools
> that was installed system-wide on the server.  Now I get this 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 1107, 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 250,
> in set_meta
>     raise Exception, "Error Setting BAM Metadata: %s" % stderr
> Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
> So, galaxy is not using the samtools from the installed galaxy package and
> is instead using the system one.  I'll try to reinstall samtools and see if
> that fixes it...

In this case Galaxy itself expects samtools on the $PATH for managing
BAM files separately from which ever tool you are using within Galaxy.

The Galaxy Tool Shed dependencies are on a per-tool basis, and not
used by Galaxy itself.

This ought to be on the wiki somewhere, but I failed to find it...

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