correct diplaying shell in help (7d881b40) · Commits · github_fork / Universc

launch_universc.sh

+10 −9

Original line number	Diff line number	Diff line
		#!/bin/bash
		#!/bin/sh

		install=false

		@@ -91,16 +91,17 @@ fi


		#####usage statement#####
		SHELL=`readlink -f /proc/$$/exe \| cut -d/ -f3`
		help='
		Usage:
		bash '$(basename $0)' --testrun -t TECHNOLOGY
		bash '$(basename $0)' -t TECHNOLOGY --setup
		bash '$(basename $0)' -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
		bash '$(basename $0)' -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
		bash '$(basename $0)' -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
		bash '$(basename $0)' -f SAMPLE_LANE1 SAMPLE_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
		bash '$(basename $0)' -v
		bash '$(basename $0)' -h
		'$SHELL' '$(basename $0)' --testrun -t TECHNOLOGY
		'$SHELL' '$(basename $0)' -t TECHNOLOGY --setup
		'$SHELL' '$(basename $0)' -R1 FILE1 -R2 FILE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
		'$SHELL' '$(basename $0)' -R1 READ1_LANE1 READ1_LANE2 -R2 READ2_LANE1 READ2_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
		'$SHELL' '$(basename $0)' -f SAMPLE_LANE -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
		'$SHELL' '$(basename $0)' -f SAMPLE_LANE1 SAMPLE_LANE2 -t TECHNOLOGY -i ID -r REFERENCE [--option OPT]
		'$SHELL' '$(basename $0)' -v
		'$SHELL' '$(basename $0)' -h

		Convert sequencing data (FASTQ) from Nadia or iCELL8 platforms for compatibility with 10x Genomics and run cellranger count