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Installation.md

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Installation

This documentation describes how to set up Shapeology on your own computer.

Step 1

Clone current github repository to your own computer. Final version:

git clone https://github.com/yoavfreund/shapeology_code.git

Current version:

git clone -b kui_dev --single-branch https://github.com/yoavfreund/shapeology_code.git

Step 2

Configuration Files

  • environ.sh: Exports the environment variables used for this project. These variables point to the directories of this deployment. Change them to your paths. Details:
# Directory where you git clone this project
export SHAPEOLOGY_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )" 
cd $SHAPEOLOGY_DIR/..
export venv=$PWD         # Directory to create virtual environment
# Directory where you save input images 
export Data_storage=change_to_your_directory   
# Directory for output results
export tmp_dir=/tmp/
# Optional, Directory for credential files of AWS and datajoint
export VAULT=change_to_your_directory

Note: Your new directories or files should be out of the project directory to avoid uploading them to Github.

  • VaultBrain (optional, for AWS use): A directory created to contain all the credential/deployment specific files for AWS and datajoint.
    • dj_local_conf.json: Specifies the credentials and the schema that is to be used for Datajoint connection. Format:
    {"database.host": your_host_address,
"database.password": your_datajoint_password,
"database.user": your_user_name,
"database.port": your_port,
"schema": your_schema_name
}
    • s3-creds.json: Specifies the credentials for AWS connection. Format:
    {"access_key": your_aws_access_key, 
"secret_key": your_aws_secret_access_key}
    • credFiles.yaml: points to the above two json files. Format:
    aws_fp: s3-creds.json
dj_fp: dj_local_conf.json
  • When configuration files are set, run the following commands to activate the environment variables and the virtual environment. Please ensure you have installed virtualenv.
source environ.sh
source virtual_env.sh

Note: Please check whether you have installed the virtual environment successfully. Clear $venv/shapeology_venv before you try again if failed.

Step 3

Test

To be continued.