SYNAPSE.md

In CRI-iAtlas/iatlas-feather-files: 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

If conda activate r-reticulate is unable to locate the environment:

1. In the R console: use conda_list() to get the list of current conda environments

R reticulate::conda_list()

1. Look for the "r-reticulate" environment path, should look like:

dataframe /<path-to-the-project-folder>/renv/python/r-reticulate/bin/python

1. Copy the env folder path of "r-reticulate" (note: leave off the /bin/python):

dataframe /<path-to-the-project-folder>/renv/python/r-reticulate

1. Activate the r-reticulate environment:

console foo@bar:~$ conda activate /<path-to-the-project-folder>/renv/python/r-reticulate

1. Inside the r-reticulate environment now, run:

(/<path-to-the-project-folder>/renv/python/r-reticulate)@user:~$ pip install synapseclient

1. The previous error should now be gone.

Synapseclient Credentials

For the login to Synapse to work correctly, there must be a .synapseCofig file in your user directory. An example file is located in the root of the application. Please see https://python-docs.synapse.org/build/html/Credentials.html for more details.

CRI-iAtlas/iatlas-feather-files documentation built on Sept. 1, 2021, 6:57 p.m.