Running GUIDE-seq in HPC¶
hpcf_interactive
export PATH=$PATH:/research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/anaconda3/condabin/
eval "$(conda shell.bash hook)"
conda activate /research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/anaconda3/envs/changeseq_py3/
module load bwa
module load samtools/1.7
module load homer/4.10
python /research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/src/guideseq_V3/guideseq/guideseq.py parallel -m test.yaml
# Below is an example to just run identify and visualization when sam files are already generated, will overwrite existing results
# python /research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/src/guideseq_V3/guideseq/guideseq.py parallel -m test.yaml --step identify+visualize
hpcf_interactive
export PATH=$PATH:/research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/anaconda3/condabin/
eval "$(conda shell.bash hook)"
conda activate /research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/anaconda3/envs/changeseq_py3/
module load bwa
module load samtools/1.7
module load homer/4.10
python /research_jude/rgs01_jude/groups/tsaigrp/projects/Genomics/common/src/guideseq_pool/guideseq/guideseq.py parallel -m test.yaml