The ICEBERG workflow middleware
Project description
ICEBERG
The master
branch generally reflects the ICEBERG release on Pypi, and is
considered stable: it should work 'out of the box'. Please refer to the documentation.
The devel
branch (and any other branches than master, for that matter)
may not correspond to the publised documentation, and specifically may have
dependencies which need to be resolved manually. Please contact us with an issue
if you need advice on the usage of any non-master branch.
Installation:
To install our package you should clone the repo by running and checkout the devel
branch:
git clone https://github.com/ICEBERG-project/ICEBERG-middleware.git
git checkout devel
Then create a Python Virtual Environment (VirtualEnv or Conda) and move in the ICEBERG-middleware folder.
To install run:
pip install . --upgrade
Usage
The ICEBERG command can be executed as follows:
iceberg [-h] [--resource RESOURCE] [--queue QUEUE] [--cpus CPUS]
[--gpus GPUS] [--input_path INPUT_PATH]
[--output_path OUTPUT_PATH] [--walltime WALLTIME]
[--analysis ANALYSIS]
{seals,penguins,4Dgeolocation,rivers,landcover} ...
The arguments shown are mandatory for the command to execute correctly. Executing with -h
will
provide the following responce:
positional arguments:
{seals,penguins,4Dgeolocation,rivers,landcover}
optional arguments:
-h, --help show this help message and exit
Required Arguments:
--resource RESOURCE, -r RESOURCE
Where the execution will happen
--queue QUEUE, -q QUEUE
The queue of the resource
--cpus CPUS, -c CPUS How many CPUs will be required
--gpus GPUS, -g GPUS How many GPUs will be required
--input_path INPUT_PATH, -ip INPUT_PATH
Where the input images are
--output_path OUTPUT_PATH, -op OUTPUT_PATH
Where the results should be saved
--walltime WALLTIME, -w WALLTIME
The estimated execution time
The expected analysis commands are:
- seals
- penguins
- 4DGeolocation
- landcover
- rivers
Based on the selected analysis further arguments may be required.
To see further help messages per use case execute the ICEBERG command with all the arguments
and add a --help
after it. It will print the arguments for the selected alanysis.
0.0.0
- Simplifying the command line interface to support subcommands
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