Updated miniconda installation steps

Error because of Linux kernel update.
IntelLabs · Dec 5, 2023 · 959ed45 · 959ed45
1 parent ba0934c
commit 959ed45
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/pipelines/deepvariant-based-germline-variant-calling-fq2vcf/setup_env.sh b/pipelines/deepvariant-based-germline-variant-calling-fq2vcf/setup_env.sh
@@ -5,11 +5,12 @@ ABS_SCRIPT_PATH="$(realpath "${SCRIPT_PATH}")"
 #echo "Value of ABS_SCRIPT_PATH: ${ABS_SCRIPT_PATH}"
 ABS_DIRECTORY="$(dirname "${ABS_SCRIPT_PATH}")"
 #echo "Value of ABS_DIRECTORY: ${ABS_DIRECTORY}"
-
+mkdir -p ./miniconda3
+ln -s ${ABS_DIRECTORY}/miniconda3 ~/miniconda3
 
 echo "Downloading and setting up miniconda..."
 wget https://repo.anaconda.com/miniconda/Miniconda3-py39_23.3.1-0-Linux-x86_64.sh
-bash ./Miniconda3-py39_23.3.1-0-Linux-x86_64.sh -b -p ./miniconda3
+bash ./Miniconda3-py39_23.3.1-0-Linux-x86_64.sh -b -u -p ./miniconda3
 echo "Downloading and setting up miniconda...DONE"
 
 echo "Seeting up conda env named with given argument"