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Basic environment setup

Development container

A lightweight development container that setups you in a matter of minutes is available here.

Manual installation

Dependencies

  • Python ≥ 3.8, < 3.13
  • Docker ≥ 24 (we recommend using Docker Desktop)
  • Java Runtime ≥ 11, ≤ 17
    • On Ubuntu, install openjdk-jre-<version> packages
  • Nextflow ≥ 23.04.0

Important

Nextflow might not detect the right Java virtual machine by default, more so if multiple versions of the runtime are installed. If so, you need to set the environment variable JAVA_HOME to target the right one.

  • Linux : look in /usr/lib/jvm for a folder named java-<version>-openjdk-<platform> and use it as JAVA_HOME.
  • MacOS : if the Java jvm is the preferential one, use JAVA_HOME=$(/usr/libexec/java_home). Else, look into /Library/Java/JavaVirtualMachines for the folder with the correct runtime version (named jdk<inner version>_1<runtime version>.jdk) and use the following : /Library/Java/JavaVirtualMachines/jdk<inner version>_1<runtime version>.jdk/Contents/Home.

Configuration

Install nf-core in your python environment (we recommend using a virtual environment) :

pip install nf-core==2.14.1

Configure your current environment so nf-core commands have access to nf-neuro modules :

export NFCORE_MODULES_GIT_REMOTE=https://github.com/scilus/nf-neuro.git
export NFCORE_MODULES_GIT_BRANCH=main
export NFCORE_SUBWORKFLOWS_GIT_REMOTE=https://github.com/scilus/nf-neuro.git
export NFCORE_SUBWORKFLOWS_GIT_BRANCH=main