From e1482006d7ccc04d2cdb64d68fc4bd90608e5e20 Mon Sep 17 00:00:00 2001 From: "jaime.ozaez" Date: Fri, 16 Aug 2024 10:41:23 +0200 Subject: [PATCH] Added loading stage for micromamba refgenie enviroment --- .../viralrecon/ANALYSIS/lablog_viralrecon | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon b/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon index 6477bd40..ec944be3 100644 --- a/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon +++ b/bu_isciii/templates/viralrecon/ANALYSIS/lablog_viralrecon @@ -205,6 +205,15 @@ check_references() { log_message "SAMtools module not loaded. Exiting..." blk_red exit 1 fi + eval "$(micromamba shell hook --shell bash)" + micromamba activate refgenie_v0.12.1 + environment=$(micromamba info | awk '/environment/ && /active/ {print $3}') + if [[ $environment == *"refgenie"* ]]; then + log_message "$environment environment succesfully activated." green + else + log_message "Refgenie environment is NOT ACTIVE. Exiting..." blk_red + exit 1 + fi if [ ! -e "/data/bi/references/refgenie/alias/${family}" ]; then # Check if directory doesn't exists log_message "Creating new directory: /data/bi/references/refgenie/alias/${family}/ and saving file ${ref}.fasta in /data/bi/references/refgenie/alias/${family}/fasta/${ref}." digest=$(openssl rand -hex 24) @@ -255,6 +264,16 @@ check_references() { if [ -z "$REF_GFF" ]; then log_message "File ${ref}.gff is not yet downloaded." if [ ! -v family ]; then obtain_family; if [ -z ${family} ]; then return; fi; fi + if [[ $environment != *"refgenie"* ]]; then + eval "$(micromamba shell hook --shell bash)" + micromamba activate refgenie_v0.12.1 + environment=$(micromamba info | awk '/environment/ && /active/ {print $3}') + if [[ $environment == *"refgenie"* ]]; then + log_message "$environment environment succesfully activated." green + else + log_message "Refgenie environment is NOT ACTIVE. Exiting..." blk_red + fi + fi if [ ! -e "/data/bi/references/refgenie/alias/${family}" ]; then # Check if directory doesn't exist log_message "Creating new directory: /data/bi/references/refgenie/alias/${family}/ and saving file ${ref}.gff in /data/bi/references/refgenie/alias/${family}/gff/${ref}." digest=$(openssl rand -hex 24)