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20 lines
758 B
Bash
20 lines
758 B
Bash
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#!/bin/bash
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# Downloads all FASTQs from a given run in cygwin
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# Get a cygwin-compatible reference to the basespace executable
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BS=$(cygpath "C:\Users\\$USER\AppData\Local\Microsoft\WindowsApps\bs.exe")
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# Prompt the user for the run id
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read -p 'Illumina Run id (not run name): ' RUNID
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# Make sure the path we want to download to exists
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mkdir -p /cygdrive/c/basespace-dl
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# Download the files
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# This monster started off from https://groups.google.com/g/basespace-developers/c/akQ0LVxxuR8/m/DhkA_4dBBAAJ
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$BS list dataset --input-run $RUNID --terse | \
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xargs -n1 -I{} $BS dataset download --id {} -o $(cygpath -w /cygdrive/c/basespace-dl/$RUNID)
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# Keep things open, in case we want to read the logs
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read -p 'Downloads completed. Press ENTER to close. ' FOO
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