Drop-seq_pipeline/Dropseq_wrapper_script.sh at master · jenni-westoby/Drop-seq_pipeline · GitHub

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#!/bin/bash

#Rename command line arguments
path_to_java=$1
path_to_ref_fasta=$2
path_to_ref_gtf=$3

./setup.sh setup
./Dropseq_Alignment_Cookbook.sh
./RSEM_ref.sh make_ref path_to_ref_gtf path_to_ref_fasta
./make_indexes.sh $path_to_ref_gtf $path_to_ref_fasta
./RSEM_three_prime_bias.sh $path_to_java

for i in Dropseq_Alignment_Cookbook/demultiplexed_fastqs/*.fastq;
do
  ./cell_level_analysis.sh $i
done


for i in Dropseq_Alignment_Cookbook/demultiplexed_fastqs/*.fastq;
do
 num_jobs=`bjobs | wc -l`
 max_jobs=100

  This prevents the number of queued jobs greatly exceeding 30.
  while [[ $num_jobs -gt $max_jobs ]];
  do
   sleep 100
   num_jobs=`bjobs | wc -l`
 done

  filename=`echo $i | awk -F/ '{print $3}'`
  ./cell_level_analysis.sh $filename
done

#make clean results matrices
 ./make_matrix.sh make_matrix RSEM
 ./make_matrix.sh make_matrix eXpress
 ./make_matrix.sh make_matrix Kallisto
 ./make_matrix.sh make_matrix Sailfish
 ./make_matrix.sh make_matrix Salmon
 ./make_matrix.sh make_matrix ground_truth
 ./make_matrix.sh make_matrix Kallisto_real
 ./clean_data.sh

#move data - some of this should move into setup.sh
cp Simulation/results_matrices/clean* raw_results/data/
cp -r Simulation/QC_stats/raw raw_results/data/
cp -r Simulation/QC_stats/simulated raw_results/data/

#format data to make figures
cd raw_results
Rscript Figure3.R
Rscript SupplementaryFigure13.R
Rscript SupplementaryFigure14.R
Rscript SupplementaryFigure15.R

cd ../figures/scripts
Rscript Figure3.R
Rscript SupplementaryFigure13.R
Rscript SupplementaryFigure14.R
Rscript SupplementaryFigure15.R