a-khalak
commented
5 years ago @cschin
Ideally, the hello world case would involve
- the user getting a set of sample reads onto their own system
- inspecting the reads in terms of how they are set up. From a .fasta or a .lst file, so they can compare to their own data.
- running the Peregrine docker, similarly to the production example but on the sample reads
- inspecting the results to confirm that they get what they would expect.
The idea is that the user should be pretty far along in terms of being able to self-serve in running their own data by more or less copying the hello world example.
cschin
huangl07
For those users that are primarily interested in running Peregrine and mainly tweaking hyperparameters, it would be helpful to have a 'hello world' runbook that walks through setting up the required inputs and running through a test case on sample data (e.g. e. coli K12).
Ideally, this would involve confirming system dependencies, obtaining some canned reads (.fasta and .lst files), running peregrine from latest stable dockerhub build, and confirming the resulting assembly.