On Wed, Nov 13, 2013 at 10:43 AM, Björn Grüning
<bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:
> Hi Peter,
>
> sorry for coming late to this thread.
>
> I may be wrong, but you are only specifying a repository_dependecies.xml
> file. You probably only need to rename it to tool_dependencies.xml file,
> otherwise the tool can not import it. I guess the env.sh file is not
> created if no tool_dependencies.xml file is present.

Yes, I think you are right about repository_dependecies.xml versus
tool_dependencies.xml but that would happen later - at this point
my tool hasn't actually tried to use samtools itself.

Thanks,

Peter

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