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ukhsa-collaboration / snapperdb

GNU General Public License v3.0
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Propose a fix to the bug leading to PICARDPATH env variable being ignored #10

Closed andersgs closed 6 years ago

andersgs commented 6 years ago

Hello.

I fixed a bug where the PICARDPATH environmental variable was being ignored, which lead to no index being produced in a new DB.

For consistency with PHEnix, I changed the variable PICARDPATH to PICARD_JAR and updated the README to reflect that.

I also corrected some minor typos in the README.

To reflect the changes, I suggested a minor version number bump to 1.0.1. I changed that in the VERSION file and in the README.

Cheers.

Anders.

andersgs commented 6 years ago

Ops. I just spotted a typo in my line directing the user to set a PICARD_JAR environmental file in the README.

Currently, it reads: Set *PICARD_JAR* - full path to the GATK Java archive.

But, perhaps should be:

Set *PICARD_JAR* - full path to the Picard Java archive.

Sorry about that.

timdallman commented 6 years ago

Accepted pull request to remove picard conflict