use python packages instead of writing shell scripts

[marrip]

I was wondering, why you decided to write shell scripts instead doing everything directly via python using maybe these packages:

• https://docs.python.org/3/library/tarfile.html
• https://gnupg.readthedocs.io/en/latest/

is it somehow slower? Or was there a particular reason why you wanted to decouple the generation from the execution?

[danielvo]

I considered the bash script a good solution for enabling the packaging/encryption outside of the Docker/Singularity image. In my limited testing, the exporting itself (the packaging + encryption) was about 25 % slower when done during the tool's runtime (I don't know whether this is an issue specific to our working environment and/or Docker, and I don't know whether it can be optimized). The extra running time would be inconvenient when a single LocalApp directory may take several hours to export (at least if we wish to export all the available FASTQ and BAM files). I thought creating a single format of bash scripts for both internal and external export was convenient (and I find the scripts easy to review/edit/re-run if necessary), but please feel free to think of suggestions for improvements to the export process.