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MorrellLAB / sequence_handling

A series of scripts to automate sequence workflows
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Edited checkVersion function in utils.sh #40

Closed EDitt closed 4 years ago

EDitt commented 5 years ago

The --version flag did not work for me for GATK (in version 4), so I edited the script to instead use the --help flag to make sure GATK was installed, and to grab the version number using the spark.jar file (which contains the version # in the filename). I also changed these things for GATK v.3 (using the --help flag and getting the version number from the help output); though I later discovered that the --version flag works just fine for the versions of GATK 3 I had available to test, so it appears to just be a specific problem with GATK 4 on my end.

EDitt commented 5 years ago

I edited these changes slightly- first, I changed the permissions back to 755. Also- I changed the function back to using the --version flag for GATK 3, however, this only works with GATK 3 when I use java jar $GATK-JAR. I commented out my first set of edits but those should still work as well.