48 lines
1 KiB
Bash
48 lines
1 KiB
Bash
#!/bin/sh
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##########################################################################
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# Script description:
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#
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# Arguments:
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#
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# Returns:
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#
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# History:
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# Date Name Modification
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# 2016-03-21 Charlie & Begin
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##########################################################################
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usage()
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{
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printf "Usage: $0 test-directory\n"
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exit 1
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}
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##########################################################################
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# Main
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##########################################################################
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if [ $# != 1 ]; then
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usage
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fi
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dir="$1"
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if [ -e "$dir" ]; then
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printf "$dir already exists. Remove it first or choose a different name.\n"
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exit 1
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fi
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cp -iR %%EXAMPLESDIR%% "$dir"
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cd "$dir"
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kallisto index -i transcripts.idx transcripts.fasta.gz
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kallisto quant -i transcripts.idx -o output -b 100 reads_1.fastq.gz reads_2.fastq.gz
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ls -l output
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more output/abundance.tsv
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cat << EOM
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See https://pachterlab.github.io/kallisto/starting.html for instructions
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on interpreting the output above.
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EOM
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