A complete 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
- nf-test ≥ 0.9.0
- Node ≥ 14,
Prettier
andeditorconfig
(see below)
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
.
The project uses poetry to manage python dependencies. To install it using pipx, run the following commands :
pip install pipx
pipx ensurepath
pipx install poetry==1.8.*
Note
If the second command above fails, pipx
cannot be found in the path. Prepend the
second command with $(which python) -m
and rerun the whole block.
Warning
Poetry doesn't like when other python environments are activated around it. Make
sure to deactivate any before calling poetry
commands.
Once done, install the project with :
poetry install --no-root
Important
Make sure no python environment is activated before running commands !
The project scripts and dependencies can be accessed using :
poetry shell
which will activate the project's python environment in the current shell.
Note
You will know the poetry environment is activated by looking at your shell. The
input line should be prefixed by : (nf-neuro-tools-py<version>)
, with <version>
being the actual Python version used in the environment.
To exit the environment, simply enter the exit
command in the shell.
Important
Do not use traditional deactivation (calling deactivate
), since it does not relinquish
the environment gracefully, making it so you won't be able to reactivate it without
exiting the shell.
Set the following environment variables in your .bashrc
(or whatever is the equivalent for your shell) :
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
This will make it so the nf-core
commands target the right repository by default. Else, you'll need to add --git-remote
and --branch
options to pretty much all commands relating to modules
and subworkflows
.
The nf-neuro
project curates a bundle of useful extensions for Visual Studio Code, the nf-neuro-extensions
package. You can find it easily on the extension
marketplace.
To install Prettier and editorconfig for the project, you need to have node
and npm
installed on your system to at least version 14. On Ubuntu, you can do it using snap :
sudo snap install node --classic
However, if you cannot install snap, or have another OS, refer to the official documentation for the installation procedure.
Under the current configuration for the Development Container, for this project, we use the following procedure, considering ${NODE_MAJOR}
is at least 14 for Prettier :
curl -fsSL https://deb.nodesource.com/setup_${NODE_MAJOR}.x | bash - &&\
apt-get install -y nodejs
npm install --save-dev --save-exact prettier
npm install --save-dev --save-exact editorconfig-checker
echo "function prettier() { npm exec prettier $@; }" >> ~/.bashrc
echo "function editorconfig-checker() { npm exec editorconfig-checker $@; }" >> ~/.bashrc