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run_multiple_samples.sh
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#!/bin/bash
sample_sheet=$1
get_mem () {
local READ1=$1
file_size_kb=$(du -Lk "$READ1" | cut -f1 | sed 's/[a-zA-Z]*//g' | sed 's/\..*//g')
if [ $file_size_kb == "" ]
then
file_size_kb=0
fi
if [ $file_size_kb -le 1000000 ]
then
mem=34
elif [ $file_size_kb -le 5000000 ]
then
mem=40
elif [ $file_size_kb -le 10000000 ]
then
mem=60
elif [ $file_size_kb -le 15000000 ]
then
mem=80
elif [ $file_size_kb -le 20000000 ]
then
mem=100
elif [ $file_size_kb -le 25000000 ]
then
mem=120
else
mem=120
fi
echo "$mem"
}
########################################################
############# HUMAN IP K27 CURIE ##################
########################################################
#CREATE CONFIG FILE : HUMAN, BEADS CURIE, IP, BED = 20k +50k
cd ~/GitLab/scNanoCutTag_10X/
while IFS= read -r line
do
# DATASET_NAME=$(echo "$line" | cut -d',' -f1)
# DATASET_NUMBER=$(echo "$line" | cut -d',' -f2)
# FINAL_NAME=$(echo "$line" | cut -d',' -f3)
# ASSEMBLY=$(echo "$line" | cut -d',' -f4)
# MARK=$(echo "$line" | cut -d',' -f5)
# if [[ $ASSEMBLY == "hg38" ]]
# then
# OUTPUT_CONFIG=/data/tmp/gjouault/results/CONFIG_HUMAN_scCutTag_10X_K27_${DATASET_NAME}
# fi
# if [[ $ASSEMBLY == "mm10" ]]
# then
# OUTPUT_CONFIG=/data/tmp/gjouault/results/CONFIG_MOUSE_scCutTag_10X_H3K27ME3_${DATASET_NAME}
# fi
# DESIGN_TYPE=LBC
# echo $DESIGN_TYPE
# echo ${ASSEMBLY}
# echo ${OUTPUT_CONFIG}
# echo ${MARK}
DATASET_NUMBER=$(echo "$line" | cut -d',' -f1)
DATASET_NAME=$(echo "$line" | cut -d',' -f2)
CLEAN_NAME=$(echo "$line" | cut -d',' -f3)
ASSEMBLY=$(echo "$line" | cut -d',' -f4)
NANOBC=$(echo "$line" | cut -d',' -f5)
MARK=$(echo "$line" | cut -d',' -f6)
DESIGN_TYPE=LBC
echo $DATASET_NUMBER
echo $DATASET_NAME
echo $CLEAN_NAME
echo $ASSEMBLY
echo $NANOBC
echo $MARK
echo $DESIGN_TYPE
FINAL_NAME=${CLEAN_NAME}_${NANOBC}_${MARK}
echo $FINAL_NAME
OUTPUT_CONFIG=/data/tmp/gjouault/results/CONFIG_scNanoCutTag_10X_${FINAL_NAME}
#Check if we can remove the -- mark
./schip_processing.sh GetConf --template CONFIG_TEMPLATE --configFile species_design_configs.csv --designType ${DESIGN_TYPE} --genomeAssembly ${ASSEMBLY} --outputConfig ${OUTPUT_CONFIG}
#--mark ${MARK}
OUTPUT_DIR=/data/kdi_prod/project_result/1184/02.00/results/scCutTag/${ASSEMBLY}/${FINAL_NAME}
#FASTQ_DIR=/data/kdi_prod/dataset/${DATASET_NUMBER}/export/user/FastqForAllSamples/
FASTQ_DIR=/data/kdi_prod/dataset/${DATASET_NUMBER}/export/user/fastqs/${DATASET_NAME}/
# FASTQ_DIR=/data/tmp/gjouault/10X/fastq/${DATASET_NAME}/
echo "cd ~/GitLab/scNanoCutTag_10X/; ./schip_processing.sh All -i ${FASTQ_DIR} -d ${DATASET_NAME} -c ${OUTPUT_CONFIG} -o ${OUTPUT_DIR} --name ${FINAL_NAME} --nanobc ${NANOBC}" | qsub -l "nodes=1:ppn=8,mem=80gb" -N job_${DATASET_NAME}_${MARK}_${ASSEMBLY}
done < "$sample_sheet"