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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

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

    reticulate::conda_list()

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

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

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

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

  4. Activate the r-reticulate environment:

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

  5. 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.