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run_everything.sh
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run_everything.sh
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base_folder=$(pwd)
echo "Running analysis in $base_folder folder"
## For singularity only, run this from command line before running this script
# module load Singualarity
# conda activate snakemake
# echo "Pulling singularity container from Github"
# singularity pull docker://ghcr.io/rasilab/burke_2022:latest
#echo "Downloading SRA annotations from GEO"
#cd $base_folder/analysis/barcode_seq/
#sh submit_cluster.sh "--snakefile" download_sra_annotations.smk "--forceall" $@
#echo "Downloading FASTQ annotations from SRA"
#sh submit_cluster.sh "--snakefile" download_fastq.smk $@
echo "Run luciferase and circular dichroism scripts"
cd $base_folder/analysis/
sh submit_local.sh "--snakefile" run_scripts.smk $@
echo "Running Pool 1 linkage analysis"
cd $base_folder/analysis/barcode_seq/pool1_linkage/scripts
sh submit_local.sh "--snakefile" get_pool1_linkage.smk $@
echo "Running Pool 1 mRNA analysis"
cd $base_folder/analysis/barcode_seq/pool1_mrna/scripts
sh submit_local.sh "--snakefile" run_pool1_mrna_barcode_count.smk $@
echo "Running Pool 1 FACS-seq analysis"
cd $base_folder/analysis/barcode_seq/pool1_facs_seq/scripts
sh submit_local.sh "--snakefile" run_pool1_facs_seq_barcode_count.smk $@
echo "Running Pool 2 linkage analysis"
cd $base_folder/analysis/barcode_seq/pool2_linkage/scripts
sh submit_local.sh "--snakefile" get_pool2_linkage.smk $@
echo "Running Pool 2 mRNA analysis"
cd $base_folder/analysis/barcode_seq/pool2_mrna/scripts
sh submit_local.sh "--snakefile" run_pool2_mrna_barcode_count.smk $@
echo "Running Pool 3 linkage analysis"
cd $base_folder/analysis/barcode_seq/pool3_linkage/scripts
sh submit_local.sh "--snakefile" get_pool3_linkage.smk $@
echo "Running Pool 3 mRNA analysis"
cd $base_folder/analysis/barcode_seq/pool3_mrna/scripts
sh submit_local.sh "--snakefile" run_pool3_mrna_barcode_count.smk $@
echo "Running Pool 4 linkage analysis"
cd $base_folder/analysis/barcode_seq/pool4_linkage/scripts
sh submit_local.sh "--snakefile" get_pool4_linkage.smk $@
echo "Running Pool 4 mRNA analysis"
cd $base_folder/analysis/barcode_seq/pool4_mrna/scripts
sh submit_local.sh "--snakefile" run_pool4_mrna_barcode_count.smk $@