IMCtransfer

A daemon to manage transference of imaging mass cytometry MCD files produced by the Hyperion instrument of EIPM, from WCM's Box.com to the SCU cluster.

It will detect new files added, maintain a database of existing files, download new files compare hashes and return the metadata of the samples.

In the future it will automatically submit jobs to process the IMC data using for example imcpipeline.

Requirements and installation

Requires Python >= 3.7.

Install with pip:

pip install git+ssh://git@github.com/elementolab/imctransfer.git

While the repository is private, the git+ssh protocol requires proper git configuration.

Running

Before running it, produce a JSON file with tokens obtained at the WCM Box.com domain:

{"client_id": "12345678901234567890123456789012",
"client_secret": "12345678901234567890123456789012",
"access_token": "12345678901234567890123456789012"}

Make sure you're the only one who can read the credentials using chmod 400. By default imctransfer looks in ~/.imctransfer.auth.json, but you can pass a custom file with the --secrets option.

Simply run without arguments on the root of the project:

imctransfer

Or specify an alternative root project directory that will be hosting the files, using the -o/--output-dir option:

imctransfer -o <directory>

To see all options, simply do:

imctransfer --help