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

guma44 / GEOparse

Python library to access Gene Expression Omnibus Database (GEO)

BSD 3-Clause "New" or "Revised" License

137 stars 51 forks source link

Open JohnWSteill opened 5 years ago

JohnWSteill commented 5 years ago

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 commented 5 years ago

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.