SYNAPSE.md

In CRI-iAtlas/iatlas-data: iAtlas Data

SYNAPSE

The iAtlas Data may depend on data from Synapse. This uses synapseclient via reticulate. The following are steps to ensure it is installed and working.

Dependencies

• Python - version < 3.7
• Miniconda

Reticulate

Reticulate should enstall as a part of the renv dependencies.

As reticulate installs, it should have a prompt that asks if you want to install miniconda. Select "Yes"

When miniconda installation finishes, you will be asked to activate the miniconda environment (from terminal)

foo@bar:~$ conda activate r-reticulate

Synapseclient

If the following error comes up:

Error in py_module_import(module, convert = convert) :
  ModuleNotFoundError: No module named 'synapseclient'

Use these steps to resolve it:

To be continued....

CRI-iAtlas/iatlas-data documentation built on July 7, 2020, 2:18 a.m.