49 lines
810 B
Bash
49 lines
810 B
Bash
#!/bin/sh
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USAGE="
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USAGE:
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viquas reference.fsa reads.bam [o r perform_richness diversity_region_length]
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"
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NUM_ARGS=$#
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case $NUM_ARGS in
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2)
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;;
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6)
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;;
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*)
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echo "${USAGE}"
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echo "Incorrect number of arguments: expecting 2 or 6"
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exit 1
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esac
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if [ ! -f "${1}" ]; then
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echo "Error: ${1} is not a file"
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exit 1
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fi
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if [ ! -f "${2}" ]; then
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echo "Error: ${2} is not a file"
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exit 1
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fi
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REFERENCE_FILE=$(basename "${1}")
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BAM_FILE=$(basename "${2}")
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cp -r /viquas/viquas_files .
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cp /viquas/ViQuaS.R .
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case $NUM_ARGS in
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2)
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Rscript ./ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}"
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;;
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6)
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Rscript ./ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}" "${@[3:]}"
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;;
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*)
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echo "${USAGE}"
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echo "Incorrect number of arguments: expecting 2 or 6"
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exit 1
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esac
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rm -rf ./viquas_files
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rm ViQuaS.R
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