locigenesis/generation.sh

#!/bin/sh

usage() {
	echo "usage: generation.sh <number of sequences> <sequencing runs>"
	exit 1
}

if [ $# != 2 ]; then
	usage
fi

sequences=$1
sequencing_runs=$2
read_mean_size=350
read_variance_size=0.0
data_directory="data/"
file="sequence.fasta"
prefix="curesim_"

Rscript src/repertoire.r "$sequences" "$sequencing_runs"
java -jar tools/CuReSim.jar -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$file" -o "$data_directory$prefix$file"
Create a script that executes the pipeline 2021-02-26 02:59:22 +01:00			`#!/bin/sh`

			`usage() {`
Add sequencing runs CLI argument 2021-02-28 02:23:58 +01:00			`echo "usage: generation.sh <number of sequences> <sequencing runs>"`
Create a script that executes the pipeline 2021-02-26 02:59:22 +01:00			`exit 1`
			`}`

Add sequencing runs CLI argument 2021-02-28 02:23:58 +01:00			`if [ $# != 2 ]; then`
Create a script that executes the pipeline 2021-02-26 02:59:22 +01:00			`usage`
			`fi`

			`sequences=$1`
Add sequencing runs CLI argument 2021-02-28 02:23:58 +01:00			`sequencing_runs=$2`
Set CuReSim read size to 350 bases 2021-03-02 20:07:05 +01:00			`read_mean_size=350`
			`read_variance_size=0.0`
Create a script that executes the pipeline 2021-02-26 02:59:22 +01:00			`data_directory="data/"`
Set CuReSim read size to 350 bases 2021-03-02 20:07:05 +01:00			`file="sequence.fasta"`
Create a script that executes the pipeline 2021-02-26 02:59:22 +01:00			`prefix="curesim_"`

Add sequencing runs CLI argument 2021-02-28 02:23:58 +01:00			`Rscript src/repertoire.r "$sequences" "$sequencing_runs"`
Set CuReSim read size to 350 bases 2021-03-02 20:07:05 +01:00			`java -jar tools/CuReSim.jar -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$file" -o "$data_directory$prefix$file"`