Tutorial feedback round 3

[nsheff]

• [x] Go down from 2 genomes to 1 to reduce external data size.
• [x] Don't write comments in code blocks. Use markdown blocks for text, code blocks for code.
• [x] what is 'CML' ?
• [x] please correct "(might have to do this before starting the tutorial)" comment
• [x] Quote below doesn't make sense to me. Where is the JSON file, in the configuration file? or is it for each bedset. I believe it should be a sample property, not a project property.

We specify a name for the bedset and a database query term that will select which BED files should belong to the bedset. The PEP configuration file must also point to a JSON file describing an Elasticsearch query to select BED files of interest.

FYI -- there was a this note:

If this hasn't been already done, we recommend starting this jupyter notebook enabling sudo permissions since steps such as downloading docker or running an elasticsearch docker container won't be executed otherwise. This can be done with sudo jupyter notebook --allow-root

I removed this because this is not necessary if you install docker correctly, adding the docker user to the sudoers group. this is outside the scope of this tutorial.

[joseverdezoto]

Quote below doesn't make sense to me. Where is the JSON file, in the configuration file? or is it for each bedset. I believe it should be a sample property, not a project property.

Each bedset config needs to point to a JSON file describing the Elastisearch query. In this case, we included a JSON test query in the bedbuncher repository, within the tests directory. It's indeed a sample property

[nsheff]

@joseverdezoto feel free to close issues when you are finished