BU-ISCIII · victor5lm · Jun 22, 2026 · Jun 22, 2026 · Jun 22, 2026 · Jun 22, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -39,6 +39,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Optimized annotation wgs & exome [#695](https://github.com/BU-ISCIII/buisciii-tools/pull/695)
 - Updated several software versions [#696](https://github.com/BU-ISCIII/buisciii-tools/pull/696)
 - Updated nextclade checks for IRMA and viralrecon [#697](https://github.com/BU-ISCIII/buisciii-tools/pull/697)
+- Enabled micromamba env activation when launching a script [#699](https://github.com/BU-ISCIII/buisciii-tools/pull/699)
 
 ### Modules
 

diff --git a/buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/05-nextclade/lablog b/buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/05-nextclade/lablog
@@ -95,7 +95,9 @@ echo "
 # Combine all results into one single file.
 echo "
   # Activate the conda environment
-  eval \"\$(micromamba shell hook --shell bash)\"
+  export MAMBA_EXE=\"/data/ucct/bi/pipelines/micromamba/bin/micromamba\"
+  export MAMBA_ROOT_PREFIX=\"/data/ucct/bi/pipelines/micromamba\"
+  eval \"\$(\$MAMBA_EXE shell hook --shell bash)\"
   micromamba activate biopython_v1.84
   echo -e \"-----Generating nextclade_combined.csv-----\"
   python3 merge_results.py

diff --git a/buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/06-variant-calling/lablog b/buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/06-variant-calling/lablog
@@ -50,7 +50,9 @@ cat ./sample_type_ref.txt | xargs -I % echo '
   awk -v id="${header_id}_${fragment}" "BEGIN{RS=\">\"; ORS=\"\"} \$0 ~ id {print \">\"\$0}" \
     ../04-irma/all_samples_completo.txt > concatenated_sequences/${sample_id}/${sample_id}_${fragment}_ref.fasta
   # Activate the conda environment
-  eval "$(micromamba shell hook --shell bash)"
+  export MAMBA_EXE="/data/ucct/bi/pipelines/micromamba/bin/micromamba"
+  export MAMBA_ROOT_PREFIX="/data/ucct/bi/pipelines/micromamba"
+  eval "$($MAMBA_EXE shell hook --shell bash)"
   micromamba activate refgenie_v0.12.1
   # Get the reference path from refgenie
   ref_path=$(refgenie seek orthomyxoviridae/fasta:${ref} -c /data/ucct/bi/references/refgenie/genome_config.yaml)
@@ -75,7 +77,9 @@ cat ./sample_type_ref.txt | xargs -I {} echo "
   mkdir -p vcf_files/\${sample_id}
   echo -e \"-----Starting \$sample_id \${fragment}-----\"
   # Activate the conda environment
-  eval \"\$(micromamba shell hook --shell bash)\"
+  export MAMBA_EXE=\"/data/ucct/bi/pipelines/micromamba/bin/micromamba\"
+  export MAMBA_ROOT_PREFIX=\"/data/ucct/bi/pipelines/micromamba\"
+  eval \"\$(\$MAMBA_EXE shell hook --shell bash)\"
   micromamba activate biopython_v1.84
   if [ -z \"\$input_file\" ]; then
     echo \"No allAlleles file found in IRMA results for \${sample_id} and \${fragment}. Skipping...\"
@@ -98,7 +102,9 @@ cat ./sample_type_ref.txt | xargs -I {} echo "
   fragment=\$(echo '{}' | awk '{print \$3}')
   mkdir -p annotated_vcfs/\${sample_id}
   # Activate the conda environment
-  eval \"\$(micromamba shell hook --shell bash)\"
+  export MAMBA_EXE=\"/data/ucct/bi/pipelines/micromamba/bin/micromamba\"
+  export MAMBA_ROOT_PREFIX=\"/data/ucct/bi/pipelines/micromamba\"
+  eval \"\$(\$MAMBA_EXE shell hook --shell bash)\"
   micromamba activate refgenie_v0.12.1
   dataDir=$(refgenie seek snpeff/flu_surveillance_db -c /data/ucct/bi/references/refgenie/genome_config.yaml)
   echo -e \"-----Annotating \$sample_id \${fragment} vcf file-----\"
@@ -119,7 +125,9 @@ cat ./sample_type_ref.txt | xargs -I {} echo "
   ref=\$(echo '{}' | awk '{print \$4}')
   fragment=\$(echo '{}' | awk '{print \$3}')
   # Activate the conda environment
-  eval \"\$(micromamba shell hook --shell bash)\"
+  export MAMBA_EXE=\"/data/ucct/bi/pipelines/micromamba/bin/micromamba\"
+  export MAMBA_ROOT_PREFIX=\"/data/ucct/bi/pipelines/micromamba\"
+  eval \"\$(\$MAMBA_EXE shell hook --shell bash)\"
   micromamba activate refgenie_v0.12.1
   dataDir=$(refgenie seek snpeff/flu_surveillance_db -c /data/ucct/bi/references/refgenie/genome_config.yaml)
   echo -e \"-----Extracting relevant fields for \$sample_id \${fragment} vcf file-----\"

diff --git a/buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/99-stats/lablog b/buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/99-stats/lablog
@@ -21,7 +21,9 @@ cat ./sample_type_ref.txt | xargs -I % echo '
 # Create a table of all the reported variants for a set of samples.
 echo "
   # Activate the conda environment
-  eval \"\$(micromamba shell hook --shell bash)\"
+  export MAMBA_EXE=\"/data/ucct/bi/pipelines/micromamba/bin/micromamba\"
+  export MAMBA_ROOT_PREFIX=\"/data/ucct/bi/pipelines/micromamba\"
+  eval \"\$(\$MAMBA_EXE shell hook --shell bash)\"
   micromamba activate biopython_v1.84
   echo -e \"-----Generating variants_long_table.csv-----\"
   python3 create_variants_long_table.py ../06-variant-calling/annotated_vcfs
@@ -30,7 +32,9 @@ echo "
 # Create a .tab file containing the percentage of Ns for each sample and each fragment.
 echo "
   # Activate the conda environment
-  eval \"\$(micromamba shell hook --shell bash)\"
+  export MAMBA_EXE=\"/data/ucct/bi/pipelines/micromamba/bin/micromamba\"
+  export MAMBA_ROOT_PREFIX=\"/data/ucct/bi/pipelines/micromamba\"
+  eval \"\$(\$MAMBA_EXE shell hook --shell bash)\"
   micromamba activate biopython_v1.84
   echo -e \"-----Generating %Ns.tab-----\"
   python3 percentajeNs.py consensus_files %Ns.tab
@@ -40,7 +44,9 @@ echo "
 # Create a table indicating the number of unambiguous bases and the total number of Ns.
 echo "
   # Activate the conda environment
-  eval \"\$(micromamba shell hook --shell bash)\"
+  export MAMBA_EXE=\"/data/ucct/bi/pipelines/micromamba/bin/micromamba\"
+  export MAMBA_ROOT_PREFIX=\"/data/ucct/bi/pipelines/micromamba\"
+  eval \"\$(\$MAMBA_EXE shell hook --shell bash)\"
   micromamba activate biopython_v1.84
   echo -e \"-----Generating qc_metrics.tsv-----\"
   # Define the input directory and the output file
@@ -81,7 +87,9 @@ echo "#!/usr/bin/env bash
   fi
 
   # Activate the conda environment
-  eval \"\$(micromamba shell hook --shell bash)\"
+  export MAMBA_EXE=\"/data/ucct/bi/pipelines/micromamba/bin/micromamba\"
+  export MAMBA_ROOT_PREFIX=\"/data/ucct/bi/pipelines/micromamba\"
+  eval \"\$(\$MAMBA_EXE shell hook --shell bash)\"
   micromamba activate refgenie_v0.12.1
 
   in=\"\$1\"

diff --git a/buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog b/buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog
@@ -1,6 +1,8 @@
 # module load singularity
 # Activate the micromamba environment
-eval "$(micromamba shell hook --shell bash)"
+export MAMBA_EXE="/data/ucct/bi/pipelines/micromamba/bin/micromamba"
+export MAMBA_ROOT_PREFIX="/data/ucct/bi/pipelines/micromamba"
+eval "$($MAMBA_EXE shell hook --shell bash)"
 micromamba activate refgenie_v0.12.1
 
 # Create folders.

diff --git a/buisciii/templates/characterization/RESULTS/lablog_characterization_results b/buisciii/templates/characterization/RESULTS/lablog_characterization_results
@@ -20,7 +20,9 @@ ln -s ../../../../ANALYSIS/*CHARACTERIZATION/*emmtyper/01-typing/results_emmtype
 
 cd ../../../
 
-eval "$(micromamba shell hook --shell=bash)"
+export MAMBA_EXE="/data/ucct/bi/pipelines/micromamba/bin/micromamba"
+export MAMBA_ROOT_PREFIX="/data/ucct/bi/pipelines/micromamba"
+eval "$($MAMBA_EXE shell hook --shell bash)"
 micromamba activate outbreakinfo
 
 python3 generate_summary_outbreak.py

diff --git a/buisciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/04-kmerfinder/lablog b/buisciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/04-kmerfinder/lablog
@@ -34,6 +34,6 @@ mv @@/data.json @@/@@_data.json
 mv @@/results.txt @@/@@_results.txt
 ln -s ../@@/@@_results.txt reports/" >> _02_kmerfinder_summary.sh
 
-echo "eval \"\$(micromamba shell hook --shell bash)\"; micromamba activate outbreakinfo" >> _02_kmerfinder_summary.sh
+echo "export MAMBA_EXE=\"/data/ucct/bi/pipelines/micromamba/bin/micromamba\"; export MAMBA_ROOT_PREFIX=\"/data/ucct/bi/pipelines/micromamba\"; eval \"\$(\$MAMBA_EXE shell hook --shell bash)\"; micromamba activate outbreakinfo" >> _02_kmerfinder_summary.sh
 echo "python3 /data/ucct/bi/pipelines/nf-core-bacass/nf-core-bacass-2.4.0/2_4_0/bin/kmerfinder_summary.py --path reports/ --output_bn kmerfinder.bn --output_csv kmerfinder_summary.csv" >> _02_kmerfinder_summary.sh
 echo "rm -rf reports" >> _02_kmerfinder_summary.sh
diff --git a/buisciii/templates/viralrecon/ANALYSIS/lablog_viralrecon b/buisciii/templates/viralrecon/ANALYSIS/lablog_viralrecon
@@ -301,7 +301,9 @@ check_references() {
             exit 1
         fi
         # Activate the micromamba environment
-        eval "$(micromamba shell hook --shell bash)"
+        export MAMBA_EXE="/data/ucct/bi/pipelines/micromamba/bin/micromamba"
+        export MAMBA_ROOT_PREFIX="/data/ucct/bi/pipelines/micromamba"
+        eval "$($MAMBA_EXE shell hook --shell bash)"
         micromamba activate refgenie_v0.12.1
         environment=$(micromamba info | awk '/environment/ && /active/ {print $3}')
         if [[ $environment == *"refgenie"* ]]; then
@@ -361,7 +363,9 @@ check_references() {
         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)"
+            export MAMBA_EXE="/data/ucct/bi/pipelines/micromamba/bin/micromamba"
+            export MAMBA_ROOT_PREFIX="/data/ucct/bi/pipelines/micromamba"
+            eval "$($MAMBA_EXE shell hook --shell bash)"
             micromamba activate refgenie_v0.12.1
             environment=$(micromamba info | awk '/environment/ && /active/ {print $3}')
             if [[ $environment == *"refgenie"* ]]; then

diff --git a/buisciii/templates/viralrecon/ANALYSIS/sgene_metrics.sh b/buisciii/templates/viralrecon/ANALYSIS/sgene_metrics.sh
@@ -1,7 +1,9 @@
 #!/bin/bash
 
 # Activate the micromamba environment
-eval "$(micromamba shell hook --shell bash)"
+export MAMBA_EXE="/data/ucct/bi/pipelines/micromamba/bin/micromamba"
+export MAMBA_ROOT_PREFIX="/data/ucct/bi/pipelines/micromamba"
+eval "$($MAMBA_EXE shell hook --shell bash)"
 micromamba activate outbreakinfo
 
 # Ensure required tools are available