jupiterPrimaryHap2Chr.pbs

#!/bin/bash
#PBS -q condo05
#PBS -l select=1:ncpus=64:mem=500GB
#PBS -l walltime=168:00:00
#PBS -W group_list=x-ccast-prj-hulke
#PBS -N JupiterPrimHap2
#PBS -j oe

set -e
set -x

# Load necessary modules
module load samtools
module load perl/5.32.0-gcc-vswq

# Activate the conda environment
source ~/miniconda3/etc/profile.d/conda.sh
conda activate base

# Set up environment variables
export PATH="/mmfs1/home/brian.smart/projects/Software/minimap2-2.28_x64-linux:$PATH"
export PKG_CONFIG_PATH=~/local/lib/pkgconfig:$PKG_CONFIG_PATH
export LD_LIBRARY_PATH=~/local/lib:$LD_LIBRARY_PATH
export PERL5LIB="/mmfs1/home/brian.smart/perl5/lib/perl5:$PERL5LIB"

# Change to the working directory
cd /mmfs1/home/brian.smart/projects/MutagenesisSmart/HudsonAlpha/JupiterPlots/PrimaryHap2Chr

# Run jupiterplot
jupiter name=PrimaryHap2Chr ref=/mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/ChrLabels17Scaffs3Assemblies/Primary_OmniCScaffolds_10Mb_17seqs_ChromosomeLabels.fa fa=/mmfs1/home/brian.smart/projects/MutagenesisSmart/HudsonAlpha/ChrLabels17Scaffs3Assemblies/Hap2_TrioChromosomes_10Mb_17seqs_ChromosomeLabels.fa t=64 m=0 ng=0 maxScaff=-1 labels=both

# You can adjust the parameters as needed. For example:
# jupiter name=myproject ref=reference.fasta fa=scaffolds.fasta t=4 ng=75 m=100000 maxGap=100000 minBundleSize=50000 MAPQ=50