genouest.md

Build app

srun --cpus-per-task=8 --mem=8G --pty bash
. /local/env/envconda.sh
conda create --name myenv
conda activate myenv
conda install -c conda-forge sbt
conda install -c conda-forge openjdk=11
git clone [email protected]:p2m2/mzxml-glucosinolate-analyser.git
cd mzxml-glucosinolate-analyser
sbt assembly

Run interactive mode

srun --cpus-per-task=8 --mem=8G --pty bash
conda activate myenv
cd mzxml-glucosinolate-analyser
java -cp ./assembly/pack.jar fr.inrae.metabolomics.p2m2.MainDetection /groups/arch_igepp/metabolomics/MassSpectrometerOutputFile/brassimet/202111/Feuilles/MzXML\ Neg/Brassinet\ F\ 33\ A\ 1500\ uL\ 0.14\ ug\ Api\ Neg_01_7781.mzXML

Run in batch mode

#!/bin/bash
#SBATCH --job-name=mzxml_gluco
#SBATCH --chdir=/home/genouest/inra_umr1349/ofilangi/workspace/mzxml-glucosinolate-analyser
#SBATCH --output=out.txt
#SBATCH --ntasks=1

# this script "script.sh" is localized in the mzxml-glucosinolate-analyser directory
. /local/env/envconda.sh
export PATH=$HOME/bin:$PATH
conda activate /home/genouest/inra_umr1349/ofilangi/sbt_env
java -cp ./assembly/pack.jar fr.inrae.metabolomics.p2m2.MainDetection /groups/arch_igepp/metabolomics/MassSpectrometerOutputFile/brassimet/202111/Feuilles/MzXML\ Neg/*.mzXML

sbatch script.sh

help

java -cp ./assembly/pack.jar fr.inrae.metabolomics.p2m2.MainDetection --help