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@phupe phupe released this 10 Feb 23:00
· 437 commits to release since this release
version-2.0.0
7e06c53

version-2.0.0
02/10/2021

NEW FEATURES

  • Tools from source:
    • they are installed in ${projectDir}/bin/fromSource in order to allow their usage inside the containers
    • the sh script which allowed the installation inside the container is not needed anymore
    • allow multi-stage building when building docker containers
  • Tools with custom install:
    • their dependencies files needed to build the containers have to be located in recipes/dependencies/label_name (to allow the -resume option)
  • New cmake options:
    • ap_linux_distro and ap_conda_release to bootstrap on containers available on 4geniac docker hub repositories (https://hub.docker.com/u/4geniac)
    • ap_mount_dir to bind folders inside containers
  • singularity profile:
    • 'autoMounts = false' when nextflow launches singularity profile
    • checkBindinds function added in singularity.config to avoid any interaction with HOME of the host for better reproducibility
    • image extension is now '.sif' instead of '.simg'
  • singularity/docker profile:
    • the conda environment is activated inside images
  • Geniac CLI:
  • Use the nextflow '-resume' options when building the configuration files en containers
  • Add params.yum to use 'dnf' instead of yum to install packages in the linux distros
  • New custom target 'build_config_files'
  • Minimal versions for nextflow (21.10.6) and singularity (3.8.5)
  • environment.yml includes all dependencies required by geniac and geniac CLI

BUGFIX

  • Copy files in /usr/local/bin in the singularity image when the tool is built from source code
  • Fix extra quotes in the beforeScript directive added in the conda.config and multiconda.config files
  • Some environment variables from the deffile were not correctly exported inside the image

DOCUMENTATION

  • How to write singularity and docker recipes to activate conda environment
  • New Miscellaneous section
  • Binary or executable script: new use cases added as onlyLinux can not always be used
  • Updates with new functionalities and modifications from version-2.0.0
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