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CDCgov / NCHHSTP-DTBE-Varpipe-WGS

This repository contains an analysis pipeline developed to characterize WGS output
Apache License 2.0
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bug in the script "get_gatk.sh" #3

Closed ybdong919 closed 1 year ago

ybdong919 commented 1 year ago

In the script "get_gatk.sh", "DL_URL=..." should be changed to "URL...". Also, "mv gatk-package-4.2.4.0-local.jar ../tools/gatk-4.2.4.0/" should be changed to "mv ./gatk-4.2.4.0/gatk-package-4.2.4.0-local.jar ../tools/gatk-4.2.4.0/ "

The corrected script is shown below:

   #DL_URL='https://github.com/broadinstitute/gatk/releases/download/4.2.4.0/gatk-4.2.4.0.zip'
   URL='https://github.com/broadinstitute/gatk/releases/download/4.2.4.0/gatk-4.2.4.0.zip'    #debug
   mkdir tmp
   cd tmp
   wget -O- $URL >gatk-4.2.4.0.zip
   unzip gatk-4.2.4.0.zip

   #mv gatk-package-4.2.4.0-local.jar ../tools/gatk-4.2.4.0/
  mv ./gatk-4.2.4.0/gatk-package-4.2.4.0-local.jar ../tools/gatk-4.2.4.0/    #debug
  cd ../
  rm -rf tmp/
reagank commented 1 year ago

This should be fixed in commit 3279dcd