jupiterHap1.pbs

#!/bin/bash
#PBS -q default
#PBS -l select=1:ncpus=16:mem=161GB
#PBS -l walltime=168:00:00
#PBS -W group_list=x-ccast-prj-hulke
#PBS -N JupiterHap1
#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/SyntenyOfAssemblies

# Debug information
ldd ~/perl5/lib/perl5/x86_64-linux-thread-multi/auto/GD/GD.so

# Run jupiterplot
jupiter name=TrioHap1 ref=Ha412HOv2_w_CPMT_trimmed_10Mb_17seqs_singleline.fa fa=Hap1_TrioScaffolds_10Mb_6seqs_singleline.fa t=16 m=0 ng=0 maxScaff=-1 labels=both