Hello Peter,

I didn't read it in the docs -- I was just assuming that the instance that runs

the functional tests would have all the dependencies installed, which appears not to be the case.

Best,

Marius

On 12 June 2015 at 10:41, Peter Cock <p.j.a.cock@googlemail.com> wrote:

On Thu, Jun 11, 2015 at 2:43 PM, Marius van den Beek
<m.vandenbeek@gmail.com> wrote:
> Hi list,
>
> I’ve been trying to write functional tests for a tool that produces BAM
> files as output. The tests run fine when using planemo locally,
> but not on the testtoolshed or on machines that do not have samtools
> installed.
> Apparently galaxy automatically tries to convert BAM to SAM to compare
> the output line by line, and so this fails. ...
>
> Should samtools perhaps be added to the list of tools required for running
> galaxy?

Hi Marius,

I thought samtools was on the list of base dependencies for Galaxy - is
it missing from somewhere you were reading (URL please)?

Thanks,

Peter