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Requirements

SAMWISE requires:

  • Nextflow
  • mamba (or conda) for automatic package installation
  • Java, which Nextflow requires and is installed automatically when installing with mamba or conda

Install mamba (or conda) first. Mamba is recommended; installation instructions are available at https://conda-forge.org/download/.

Install Nextflow from the Bioconda package. We recommend using a separate environment rather than the base environment:

mamba install -n nextflow -c bioconda nextflow
mamba activate nextflow

Nextflow can also be installed through the Bioconda Nextflow package.

Clone SAMWISE after installing the prerequisites, or download and extract the repository in the location of your choice:

git clone https://github.com/PNNL-SoilSFA/samwise.git

Source and results directories

Use --samwise_dir for the SAMWISE source directory and --working_dir for workflow results, generated environments, and downloaded tool databases:

nextflow run /path/to/samwise/module_0_readprocess.nf \
  --samwise_dir /path/to/samwise \
  --working_dir /path/to/samwise-results

The downloaded samwise directory contains the Nextflow workflows, helper scripts, and bundled dependencies. The directory options have these fallback rules:

  • Supplying both parameters keeps source code under --samwise_dir and results, created environments, and downloaded databases under --working_dir.
  • Supplying only --working_dir uses the directory containing the launched workflow as samwise_dir; results and code are under --working_dir.
  • Supplying only --samwise_dir uses that source directory as the default working_dir; results and code are under --samwise_dir.

For separate source and results directories, invoke the workflow by its absolute path as shown above.