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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