Intricacies of for loops in jupyter notebook

[laurahspencer]

I'm running for loops in a Jupyter Notebook using bash and have encountered a couple issues:

1. Can't figure out how to redirect the output to a text file. I've tried the suggestions listed in this stackoverflow post, but none have successfully worked. Here's an example of my attempt - also tried >> out.txt inside the loop before done.

2. A variable I set outside the loop (path to a program) isn't working inside the loop

[sr320]

1. I think you want to write out standard error prior to done

2> $file.err

2. does not seem to be an impediment?

If you post jupyter nb on github I can troubleshoot.

[kubu4]

1. What @sr320 said.

2. Agree with @sr320 . Also, I don't see that variable defined in that cell. Is it defined earlier in the notebook? Note, @yaaminiv had/has an issue with using variables defined outside of her current cell (https://github.com/RobertsLab/resources/issues/488#issuecomment-439194085) as well.

[laurahspencer]

1. This is what worked (outside of loop): done >> bowtieout.txt 2>&1

2. Not an impediment, just annoying. The variable defined previously works between cells, but not within the loop. Oh well!