Make commands

Multiple commands are already pre-implemented. They will allow you to perform a lot of steps in a single time, also avoiding recomputing unnecessary steps. Globally, we organized the lotus-processor with 4 modes:

Full

The mode we run internally. It is heavily time- and memory-consuming. If running from scratch, expect to have about 40mio entries processed

• Expected runtime: days.

⚠️ We do not recommend running this mode except you want to try reproducing our whole set.

make MODE=full lotus-roots

Min

An intermediate mode running on 500 entries. It will gather all easily accessible resources and sample 500 entries randomly.

• Expected runtime: <20min (depending on your internet connexion).

⚖️ We only recommend this mode if you are interested in more than the test mode.

make MODE=min lotus-seeds

Test

A brief mode going through the whole process to ensure everything is running smoothly.

• Expected runtime: <5min

✅ We recommend you start with a test before going deeper into the process.

make MODE=test lotus-bloom
make MODE=test lotus-check

Custom

The mode that will prepare your own documented structure-organism pairs.

• Expected runtime: fast, depending on how many documented pairs you have.

😍 Thank you for using this mode, the community will appreciate using your data!

cd src
Rscript 1_gathering/db/custom/standardizing.R <path_to_your_file>
cd ..
make MODE=custom lotus-bloom

Compatibility matrix

As we mix modes and targets, we provide hereafter some guidance on how to combine them:

	lotus-check	lotus-bloom	lotus-seeds	lotus-roots
MODE = test	✅	✅	⚠️	⚠️
MODE = custom	⛔	✅	⚠️	⚠️
MODE = min	⛔	✅	✅	⚠️
MODE = full	⛔	⚠️	⚠️	✅

✅ = We advise this combination

⚠️ = We do not advise this combination, it can work but makes no real sense

⛔ = This combination can not work