velocityscript.sh

#!/bin/bash
exec 3>&1 4>&2
trap 'exec 2>&4 1>&3' 0 1 2 3
exec 1>log.out 2>&1
## get folder names and store in array
files=( $(aws s3 ls s3://fertig-lab-bucket/projects/Short_Time_Course_Single_Cell/fileGroups/ | awk '{print $4}') )
#folders=( ${folders[@]:2} )
#echo ${folders[@]}

# download fileGroup files
for file in ${files[1]}; do
        #download one file SXX_L00X.txt
        echo downloading file $file
        aws s3 cp s3://fertig-lab-bucket/projects/Short_Time_Course_Single_Cell/fileGroups/${file} ./
        fastqFiles=( $(awk '{print $1}' $file))
        folderName=$(echo $file | tr -d '.txt' | cat)
        echo making folder $folderName
        mkdir $folderName
        rfq=()
        for fq in ${fastqFiles[@]}; do
                fq=$(echo $fq | tr -d '\040\011\012\015' | cat)
                aws s3 cp s3://fertig-lab-bucket/projects/Short_Time_Course_Single_Cell/${fq} ${folderName}/
                if echo $fq | grep _R; then
                        rfq+=( $fq )
                fi
        done
        echo removing folder $folderName
        #rm -r $folderName
        echo removing file $file
	rm $file
done
# dowload the files in a group

# run kb and store output in a folder

# delete fileGroup file and downloaded files

# # start loop to perform kallisto bus
# for name in ${folders[@]}; do
# 	echo creating directory $name
# 	mkdir $name
# 	# list files on aws
# 	files=( $(aws s3 ls s3://fertig-lab-bucket/projects/Evanthia_MDSC_Analysis/$name | awk '{print $4}' | grep _R) )
# 	for file in ${files[@]}; do
# 		#echo $name$file
# 		#download files from aws
# 		aws s3 cp s3://fertig-lab-bucket/projects/Evanthia_MDSC_Analysis/$name$file $name
# 	done
# 	echo Running kallisto bustools
# 	kb count -i mouse_velocity_index2/index.idx -o output_$name -x 10xv2 -t 36 -g mouse_velocity_index2/transcripts_to_genes.txt \
# 	 -c1 mouse_velocity_index2/cdna_transcripts_to_capture.txt -c2 mouse_velocity_index2/intron_transcripts_to_capture.txt --lamanno \
# 	  --h5ad $name${files[0]} $name${files[1]} $name${files[2]} $name${files[3]}
# 	echo Generated spliced and unspliced data for $name
# 	echo deleting directory $name
# 	rm -r $name
# 	echo uploading output folder to aws
# 	aws s3 cp output_$name s3://fertig-lab-bucket/projects/Evanthia_MDSC_Analysis/output_$name --recursive
# 	echo deleting output folder
# 	rm -r output_$name
# done
#