setup envBarcodeMiner

you need apptainer (https://apptainer.org/) load on ip34: ml StdEnv/2023 apptainer/1.3.5

export INSTALLATION_PATH=/fast/def-ilafores/
export ENVBARCODEMINER_PATH=${INSTALLATION_PATH}/envBarcodeMiner
cd ${INSTALLATION_PATH}
git clone [email protected]:jflucier/envBarcodeMiner.git

setup dicey container

cd ${ENVBARCODEMINER_PATH}
cd containers
singularity build --force --fakeroot envBarcodeMiner.sif envBarcodeMiner.def

setup db

cd ${ENVBARCODEMINER_PATH}
sh install_db.sh

analysis example

export ANALYSIS_PATH=/fast/def-ilafores/20250318_envBarcodeMiner_test
cd ${ANALYSIS_PATH}

show help message

sh /fast/def-ilafores/envBarcodeMiner/run_envBarcodeMiner.local.sh -h

sh /fast/def-ilafores/envBarcodeMiner/run_envBarcodeMiner.local.sh -t 12 \
-o $PWD -primer_f CTTGGTCATTTAGAGGAAGTAA -primer_r GCTGCGTTCTTCATCGATGC

Run with degenerate pairs

mkdir -p primer_pairs
bash $ENVBARCODEMINER_PATH/dedegenerate.sh CYGTRCDAAGGTAGCATA TARTYCAACATCGRGGTC primer_pairs/all_primers.tsv

while read -r FWD REV; do
    OUT_DIR=$ANALYSIS_PATH/primer_pairs/${FWD}_${REV}
    #if [[ -f $OUT_DIR ]]
    mkdir -p $OUT_DIR
    nice sh $ENVBARCODEMINER_PATH/run_envBarcodeMiner.local.sh -t 36 -o $OUT_DIR -primer_f $FWD -primer_r $REV
done < primer_pairs/all_primers.tsv