Installation
SIMPLI relies on Nextflow DSL2 syntax and requires nextflow >= 20.07.1
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Install Singularity and add it to $PATH:
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Install Nextflow and add it to $PATH:
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Clone the SIMPLI repository to the desired folder:
git clone https://github.com/ciccalab/SIMPLI.git PATH_TO_DESIRED_FOLDER
In alternative, the most recent version of SIMPLI be downloaded and run from directly from this repository with:
nextflow run https://github.com/ciccalab/SIMPLI [COMMAND_LINE_ARGUMENTS] [NEXTFLOW_OPTIONS]
See the Nextflow documentation for more details.
SIMPLI can be run in High Performance Computing (HPC) environments using Nextflow to automatically manage job submission. See the run page for details on the available profiles.
SIMPLI has not been tested to run on Apple M1 chip, and compatible Singularity images for ARM64 architecture need to be compiled. The container definition files are available at the Singularity recipes folder. Once compiled the containers, it is necessary to modify the processes.nf file to point to the local versions of the containers.
An example workflow can be run as a test with:
nextflow main.nf -profile test
From the directory SIMPLI is installed in.
See the example analysis page for more details.