Requirements:
- samtools
- arriba
Create a conda environment with the required packages:
conda config --add channels r
conda config --add channels bioconda
conda config --add channels conda-forge
conda create --n arriba
conda activate arriba
conda install -c bioconda arriba
conda install -c bioconda samtools
Run the pipeline
qsub ExtractSamples.sh batchid
list=$(cat samples_batchid.txt )
for l in $list; do echo ${l}; qsub Alignment.sh ${l} batchid; done
for l in $list; do echo ${l}; qsub ProteinCalling.sh ${l} batchid; done
for l in $list; do echo ${l}; qsub CheckAlignReads.sh ${l} batchid; done