Download anaconda and install it : https://www.anaconda.com/products/individual
create a new environment conda create -n irods-env python=3.9
Activate the environment conda activate irods-env
pip install python-irodsclient
pip install numpy pip install pandas pip install xlrd
usage: microirods [-h] {info,upload,remove} ...
Manage microscopy images with IRODS
positional arguments:
{info,upload,remove}
info Get info from a iRODS destination
upload Upload a file of files in a directory to an iRODS
destination
remove Remove a file in an iRODS destination
optional arguments:
-h, --help show this help message and exit
Process finished with exit code 0
usage: microirods upload [-h] --destination DESTINATION --source SOURCE
--irods_session IRODS_SESSION [--metadata METADATA]
[--file_extensions FILE_EXTENSIONS]
optional arguments:
-h, --help show this help message and exit
--destination DESTINATION
iRODS destination
--source SOURCE source file/folder
--irods_session IRODS_SESSION
The path to the iRODS environment JSON file
--metadata METADATA metadata file
--file_extensions FILE_EXTENSIONS
File extensions to upload, e.g. nd2 or multiple one
separated by comma, e.g. tif,tiff,czi
python micro_irods upload --irods_session C:\Users\myuser\.irods\irods_environment.json --destination /irods/environment --source test_dataset\ --file_extension tif,czi --metadata test_dataset\metadata.xlsx