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README_dev.md

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Compilation

sbt assembly

Tools

JAR=assembly/$(ls  assembly/ | tail -n1)

Gcms2Isocor

COMMAND="fr.inrae.metabolomics.p2m2.command.GCMS2IsocorCommand"
java -cp $JAR $COMMAND --help
java -cp $JAR $COMMAND src/test/resources/GCMS/13CPROT1.txt src/test/resources/GCMS/13CPROT2.txt --out input_isocor.tsv

Input Data / GCMS PostRun Analysis

Export Data -> Compound Quantitative Results

Header - Name format

name -> extraire (metabolite/derivative/isotologue)

example glycosate / TMS / m0

"sample""replicat""passeur"

OpenLabCDS2Csv

COMMAND="fr.inrae.metabolomics.p2m2.command.OpenLabCDS2CsvCommand"
java -cp $JAR $COMMAND --help
java -cp $JAR $COMMAND src/test/resources/OpenLabCDS/Report_Ex1.txt src/test/resources/OpenLabCDS/Report_Ex2.txt src/test/resources/OpenLabCDS/Report_Ex3.txt --out text.csv


COMMAND="fr.inrae.metabolomics.p2m2.command.MassLynx2IsocorCommand"
java -cp $JAR $COMMAND --help
java -cp $JAR $COMMAND src/test/resources/MassLynx/mass_15Ngly.txt -d src/test/resources/MassLynx/correspondence_derivatives.txt --out input_isocor.tsv

Create conda package

conda-build conda-recipe

Testing package

doc : https://bioconda.github.io/contributor/building-locally.html

conda create --use-local -n test p2m2tools
conda activate test

p2m2tools fr.inrae.metabolomics.p2m2.command.OpenLabCDS2CsvCommand --help

commands

  • fr.inrae.metabolomics.p2m2.command.OpenLabCDS2CsvCommand
  • fr.inrae.metabolomics.p2m2.command.GCMS2IsocorCommand
  • fr.inrae.metabolomics.p2m2.command.MassLynx2IsocorCommand

circle-ci

circleci config validate circleci config process .circleci/config.yml circleci local execute --job compile circleci local execute --job test_and_coverage_jvm