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Building MuTect 1.1.7?
I tried to build the latest MuTect according to the readme available at https://github.com/broadinstitute/mutect and I ran into an error. Specifically, there is an error building gatk-protected only if I include the git reset --hard 3.1.
git reset --hard 3.1
(comment) build the GATK first and install it to the local mvn repo.
mvn -Ddisable.queue install
If I do not include the git reset --hard 3.1 then gatk-protected will build fine, but then
(comment) build MuTect
does not work and reports errors about needing gatk repository/dependencies.
Has something changed recently that interferes with building MuTect, or am I doing something wrong?