Add iRODS support to dtool
Project description
Free software: MIT License
Features
Copy datasets to and from iRODS
List all the datasets in an iRODS zone
Create datasets directly in iRODS
Installation
To install the dtool-irods package.
pip install dtool-irods
Usage
To copy a dataset from local disk (my-dataset) to an iRODS zone (/data_raw) one can use the command below.
dtool copy ./my-dataset /data_raw irods
To list all the datasets in an iRODS zone one can use the command below.
dtool ls /data_raw irods
See the dtool documentation for more detail.
Configuring the local dtool iRODS cache
When fetching items from a dataset, for example using the dtool item fetch command, the content of the item is cached in a file on local disk. The default cache directory is ~/.cache/dtool/irods.
One may want to change this directory. For example, if working on a HPC cluster to set it to a directory that lives on fast solid state disk. This can be achieved by setting the DTOOL_IRODS_CACHE_DIRECTORY environment variable. For example
mkdir -p /tmp/dtool/irods
export DTOOL_IRODS_CACHE_DIRECTORY=/tmp/dtool/irods
Alternatively, when using the dtool command line interface one can add the DTOOL_IRODS_CACHE_DIRECTORY key to the ~/.config/dtool/dtool.json file. For example,
{
"DTOOL_IRODS_CACHE_DIRECTORY": "/tmp/dtool/irods"
}
If the file does not exist one may need to create it.
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