BPA to Galaxy repo to store early POCs and other relevant documents
- If already installed skip step 1
sudo apt install python3-venv
- Run python3 command to create virtual environment
python3 -m venv my-anyname-env
- Modify env files as required then source each one
source bpatogalaxy.env
source bpatogalaxy_settings.env
- Activate your python virtual env
source my-anyname-env/bin/activate
- Install python libraries inside your virtual as required
pip install bioblend
pip install ckanapi
pip install webdavclient3
- Run POCs passing the right parameters
python3 upload_file_aws_presigned_url_libraries.py $BIOBLEND_GALAXY_URL $BIOBLEND_GALAXY_API_KEY $AWS_PRESIGNED_URL
python3 upload_file_aws_presigned_url_histories.py $BIOBLEND_GALAXY_URL $BIOBLEND_GALAXY_API_KEY $AWS_PRESIGNED_URL
python3 upload_file_ckan_api.py $BIOBLEND_GALAXY_URL $BIOBLEND_GALAXY_API_KEY $BPA_PORTAL_URL $BPA_PORTAL_KEY $BPA_PORTAL_FYLE_TYPE $BPA_PORTAL_FILE_NAME
python3 poc_bpa_cloudstor.py $CLOUDSTOR_URL $CLOUDSTOR_USER $CLOUDSTOR_KEY $CLOUSTOR_DIR $BPA_PORTAL_URL $BPA_PORTAL_KEY $BPA_PORTAL_FYLE_TYPE $BPA_PORTAL_FILE_NAME $LIST_FILES_ONLY $UPLOAD_FROM_LOCAL $LIST_FILES_ONLY $UPLOAD_FROM_LOCAL
- Deactivate your virtual env using below command
deactivate