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Warning if fastq-dump is not installed or on $PATH #58

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JohnWSteill opened this issue Apr 9, 2019 · 1 comment
Open

Warning if fastq-dump is not installed or on $PATH #58

JohnWSteill opened this issue Apr 9, 2019 · 1 comment

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@JohnWSteill
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Great package, thanks!

I lost a bit of time tracking down fastq-dump error with the download_SRA() function.

Granted,

"09-Apr-2019 12:48:02 ERROR sra_downloader - fastq-dump command not found"

is pretty good, but maybe it would be nice to see a good exception raised before the 15Gb file dowload?

Again, awesome pkg, thanks!

Best,

John

@guma44
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guma44 commented Apr 10, 2019

Hi, that is good point. Could you send a snippet (if it is not confidential)? Anyway, I think this is something that could be fastly done.

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