#!/bin/bash -l
#
#$ -cwd
#$ -j y
#$ -P waxmanlab
#$ -m be
#$ -M kkarri@bu.edu
#$ -N mm10_pcg-only_usethis
#$ -pe omp 8
#$ -l mem_per_core=2G
#$ -l h_rt=72:00:00
echo "=========================================================="
echo "Starting on       : $(date)"
echo "Running on node   : $(hostname)"
echo "Current job ID    : $JOB_ID"
echo "Current job name  : $JOB_NAME"
echo "Task index number : $TASK_ID"
echo "=========================================================="


source ~/.bashrc
#old version used to run tabula muris data
#module load bcl2fastq/2.20
#module load cellranger/2.1.1

module load bcl2fastq/2.20
module load cellranger/3.1.0


cellranger mkref --genome="mm10_premrna_v1.0_pcg-only" --fasta="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/genome.fa" --genes="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm10_ensmbl/GRCh38-1.2.0.gene.premrna.filtered_v1.1.gtf"

#cellranger mkref --genome="mm9_usethis" --fasta="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm9/mm9_plus.fa" --genes="/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/ref/mm9/Refseq-lnc_GeneBody_mcherry-dcas9-krab-ERCC_mm9.gtf"
echo "Finished  .............. $(date)"