Hi, I try to follow the build intructions in the MuTect github Readme. It seems to build fine but the packaging does not work (see log attached). When I do a "dist" instead of "package" ant runs through but the only classes related to MuTect in the jar seem to be the queue extensions. Strange.. I wonder if I am doing something wrong?
Hi -- I'm not sure what the trouble is that you're having. I just took the instructions from the GitHub Readme and ran them on a clean machine and everything was ok.
I noticed in your build output it says:
[echo] Include External? : no
Which means either you didn't run with the specified command (ant -Dexternal.dir=pwd/../mutect-src -Dexecutable=mutect package)
or that the mutect-src isn't in the right place relative to the gatk dir. the external.dir above should point to the directory ABOVE the mutect directory. So if you run "ls -l pwd/../mutect-src" you will see:
bm5fb-3a0:~/andre/gatk-protected [master*] $ ls -l pwd/../mutect-src
drwxr-xr-x 14 kcibul CHARLES\Domain Users 476 Oct 25 21:14 mutect
Hope this helps
Thanks for the help. Actually it was an issue with the directory structure. So just for reference, the correct one ist:
top_level /mutect-src /mutect /gatk-protected
I probably got confused by the order in which the two repositories are cloned. Anyway, thanks again.