A lightweight development container
that setups you in a matter of minutes is available here.
- Python ≥ 3.8, < 3.13
- Docker ≥ 24 (we recommend using Docker Desktop)
- Java Runtime ≥ 11, ≤ 17
- On Ubuntu, install
openjdk-jre-<version>
packages
- On Ubuntu, install
- 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 namedjava-<version>-openjdk-<platform>
and use it asJAVA_HOME
. - MacOS : if the
Java jvm
is the preferential one, useJAVA_HOME=$(/usr/libexec/java_home)
. Else, look into/Library/Java/JavaVirtualMachines
for the folder with the correct runtime version (namedjdk<inner version>_1<runtime version>.jdk
) and use the following :/Library/Java/JavaVirtualMachines/jdk<inner version>_1<runtime version>.jdk/Contents/Home
.
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