moved the set -o lines under the ACCESS_TOKEN block #133
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Performed a test on a full dataset and confirmed that the varscan results are identical (except for expected differences including file paths and time stamps). |
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Attempting to run immuno on compute1 results in varscan failing. @tmooney suggested moving the set -o lines after the wget block. As of now, since errext and pipefail are set before wget, when the command is executed wget does not find the server and it causes a non-zero exit. I have tested this change and it appears that this fix allows varscan to execute successfully.