Marechal_pipelines

SSh config for running on remote host gh1301.m

Host gh1301
  Hostname gh1301.m
  user maxl
  ServerAliveInterval 600
  Compression yes
  IdentityFile ~/.ssh/id_rsa
  ProxyJump ip34.ccs.usherbrooke.ca

Clone Repo

git clone --recurse-submodules --branch=main  git@github.com:jflucier/Marechal_pipelines.git

cd ./Marechal_pipelines

Create a Virtual env :

python3.12 -m venv venv
. venv/bin/activate
numpy==2.2.3
pandas==2.2.3
cd ./DryPipe
pip install -e .
cd ..

Setup an init script for your particular pipeline instance

Follow the example: ./example/env-il2_inversefold.sh

It's a virtualenv init script for running pipelines instances from directory ./example

cd ./example

mkdir MyPipelineInstanceDir

# create samplesheet in ./MyPipelineInstanceDir/samplesheet.tsv

# init virtual env :

. ./env-il2_inversefold.sh `pwd`/MyPipelineInstanceDir

drypipe run