Fast Installation

Easy install method

Enter this command in your terminal (it downloads the container and Extractor_flow code in the current directory - Make sure nextflow is already installed before running this command):

curl -s https://Extractor_flow-documentation.readthedocs.io/en/1.0.0/install.sh | bash

Detailed Installation

Extractor_flow pipeline

Release

Download Extractor_flow pipeline:

$> nextflow pull scilus/extractor_flow

For developers

Clone Extractor_flow pipeline repository:

# Clone with HTTPS
$> git clone https://github.com/scilus/extractor_flow.git

# Clone with SSH
$> git clone git@github.com:scilus/extractor_flow.git

As a developer you will have to run Extractor_flow using this command:

nextflow run extractor_flow/main.nf --help

Singularity for Extractor_flow

Release

Download the last release of the Singularity container for Extractor_flow:

$> wget https://scil.usherbrooke.ca/containers/scilus_flows_1.5.0.sif

Or if you have sudo privileges

$> sudo singularity build scilus_flows_1.5.0.sif docker://scilus/scilus:1.4.2

For developers

Clone the singularity repository for Extractor_flow pipeline:

# Clone with HTTPS
$> git clone https://github.com/scilus/containers-scilus.git

# Clone with SSH
$> git clone git@github.com:scilus/containers-scilus.git

Then, you can build the singularity image:

$> singularity build scilus_flows_1.5.0.sif singularity_scilus.def

Docker for Extractor_flow

First, change the number of CPUs and RAM (recommended: 8 CPUs and 16Gb of RAM) in Docker (Preferences -> Advanced) and click on Apply & Restart.

Download the last release of the Docker container for Extractor_flow:

$> docker pull scilus/scilus:1.4.2

Please see Profiles section to use macos profile.