Differential D13328 Diff 36120 head/biology/kallisto/files/kallisto-test.in

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Standalone View

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svn:eol-style	null	native \ No newline at end of property
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				#!/bin/sh

				##########################################################################
				# Script description:
				#
				# Arguments:
				#
				# Returns:
				#
				# History:
				# Date Name Modification
				# 2016-03-21 Charlie & Begin
				##########################################################################

				usage()
				{
				printf "Usage: $0 test-directory\n"
				exit 1
				}


				##########################################################################
				# Main
				##########################################################################

				if [ $# != 1 ]; then
				usage
				fi

				dir="$1"
				if [ -e "$dir" ]; then
				printf "$dir already exists. Remove it first or choose a different name.\n"
				exit 1
				fi

				cp -iR %%EXAMPLESDIR%% "$dir"
				cd "$dir"
				kallisto index -i transcripts.idx transcripts.fasta.gz
				kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz
				ls -l output
				more output/abundance.tsv

				cat << EOM

				See https://pachterlab.github.io/kallisto/starting.html for instructions
				on interpreting the output above.

				EOM