Pipeline for parrallel Anvi'o on HPC (PBS scheduler)
This pipeline requires to download and install anvio v6on the HPC.
This pipeline requires to download and install anvio v6on the HPC.
please modify the
-
DIR= Directory of contigs to process
-
SAMPLE_LIST= List of samples to process
-
RAW_DIR= directory containing raw fastq files
-
MAIL_USER = indicate here your arizona.edu email
-
GROUP = indicate here your group affiliation
You can also modify
- BIN = change for your own bin directory.
- MAIL_TYPE = change the mail type option. By default set to "bea".
- QUEUE = change the submission queue. By default set to "standard".
Raw files should be as follow ${SAMPLE}_R1_QC.fq and ${SAMPLE}_R2_QC.fq Contigs should be as follow ${SAMPLE}_contigs.fa
Run
./submit.sh
This command will place two jobs in queue.