On Wed, Nov 13, 2013 at 10:43 AM, Björn Grüning firstname.lastname@example.org wrote:
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.