How to write a bash script for your reproducible data analysis pipeline (CC247)

[@haraldurkarlsson1147]

Very interesting. I tend to simply just run curl in the Mac terminal rather than a script. But I only upload these occationally.

[@leonelemiliolereboursnadal6966]

Thanks again!! you are the best man!, 🙌🙌

[@Riffomonas]

My pleasure!🤓

[@musicspinner]

Great stuff. Looking forward to seeing snakemake in action. 👍🏽

[@Riffomonas]

Thursday! Thanks for watching 🤓

[@mdeeaonetwothree5162]

This tutorial uses the Windows based Visual Studio to demonstrate Snakemake. It gives some great tips on reproducibility and gives good examples on interpreting and fixing error messages as part of a small project. Shows how to test rules individually. Does not demonstrate parallelisation. The creation of the DAG was interesting.

[@Riffomonas]

Thanks for watching!

[@metameles5846]

-O lets you overwrite an existing file. Have a good day.

[@tomaszkrukowski1393]

wget -N prevents the same files from being downloaded again if they have not changed (by checking timestamping)

[@markrandall7631]

I have been trying this and some URL exit without the URL in single quotes and some need single quote URL to exit. Gone to encapsulating all URL in single quotes.

[@Riffomonas]

yeah bash can sometimes do different things with single vs double quotes. a backslash can be useful for escaping quotes if you need to have quotes in quotes

[@markrandall7631]

@@Riffomonas this was without the URL in any quotes, like your script.

[@qwerty11111122]

dollar outside curly braces?

[@Riffomonas]

Yeah I couldn’t think fast enough 😂

[@qwerty11111122]

@@Riffomonas I feel that

[@dubhsith5993]

Odd that someone would load Tidyverse and then use bash to script the download of files :)

[@Riffomonas]

🤷‍♂️there’s pedagogy baked into everything. Thanks for watching!