Hello Peter,

I didn't read it in the docs -- I was just assuming that the instance that
the functional tests would have all the dependencies installed, which
appears not to be the case.


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

> On Thu, Jun 11, 2015 at 2:43 PM, Marius van den Beek
> <m.vandenb...@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
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