Releases | Open Source Science

https://github.com/bioinfo-pf-curie/geniac - version-3.7.0

version-3.7.0 05/23/2025

NEW FEATURES - almalinux:9.5 set as default for the containers - remove the use of the defaults conda channel to comply with anaconda license: * conda 24.11.3-2 from miniforge set as default for the containers * options '--condaNoDefaultsChannel' can to passed to nextflow to include the defaults conda channel in the yml files automatically generated by geniac - git: geniac checks for production tage with patterns 'version-1.2.3' or 'v1.2.3' - the geniac conda env does not use the defaults channel but the nodefaults channel - Geniac CLI: * remove the use of the defaults conda channel to comply with anaconda license: * Check that the defaults channel is not used to comply with anaconda license * option 'condaNoDefaultsChannel' in geniac.ini file allows the use of the defaults conda channel if needeed

- Python
Published by phupe about 1 year ago

https://github.com/bioinfo-pf-curie/geniac - version-3.6.0

version-3.6.0 01/10/2025

NEW FEATURES - Geniac CLI: * Environment variables from the user space are passed to the sudo command * Conda env with nextflow 24.04.4, pip 24.2, make 4.4.1, python 3.12.5 * geniac must be installed using pip after the geniac conda env is created

BUGFIX - Geniac CLI: * Both ADD and COPY directives in Dockerfile are considered to check file dependencies

- Python
Published by phupe over 1 year ago

https://github.com/bioinfo-pf-curie/geniac - version-3.5.0

version-3.5.0 08/27/2024

NEW FEATURES - a sha256sum signature is generated for each container recipe (including its dependencies). The list of signatures is provided both as global file (sha256sum) and individual files for each tool (eg python.sha256sum) - new cmake option 'apcontainerlist' to build only a subset of container provided as a list in a txt file.

- Python
Published by phupe almost 2 years ago

https://github.com/bioinfo-pf-curie/geniac - version-3.4.0

version-3.4.0 08/08/2024

NEW FEATURES - nextflow scripts have been migrated to DSL2 - Geniac CLI: * Return exit code 1 on any error with the CLI.

- Python
Published by phupe almost 2 years ago

https://github.com/bioinfo-pf-curie/geniac - version-3.3.0

version-3.3.0 04/12/2024

NEW FEATURES - almalinux:9.3 set as default for the containers - conda 23.10.0 set as default for the containers

- Python
Published by phupe about 2 years ago

https://github.com/bioinfo-pf-curie/geniac - version-3.2.1

version-3.2.1 10/12/2023

BUGFIX - singularity/docker profiles: * post commands were written twice in the recipes generated by geniac

- Python
Published by phupe over 2 years ago

https://github.com/bioinfo-pf-curie/geniac - version-3.2.0

version-3.2.0 09/08/2023

NEW FEATURES - singularity/docker profiles: * params.yumOptions added ine the nextflow.config file, and options set with '--setopt=fastestmirror=1 --setopt=metadata_expire=0' - new profile created by geniac: apptainer (since 'apptainer.enabled' has been introduced in nextflow 23.04.0) - Geniac CLI: * 'geniac lint': consider that the nextflow pipeline is implemented using DSL2. Modifications have been made only for process using renv. 'geniac lint' could still work on DSL1 pipeline provided that there is no process using renv. * Update conda env with new tool versions

- Python
Published by phupe almost 3 years ago

https://github.com/bioinfo-pf-curie/geniac - version-3.1.0

version-3.1.0 08/14/2023

NEW FEATURES - almalinux:8.8 set as default for the containers - conda 25.3.1 set as default for the containers - micromamba is used to create conda envs and install conda packages - conda/multiconda profiles: * conda.enable has been added - Geniac CLI: * Conda env with apptainer 1.2.2, nextflow 22.10.6, pip 23.2.1

- Python
Published by phupe almost 3 years ago

https://github.com/bioinfo-pf-curie/geniac - version-3.0.0

version-3.0.0 05/05/2023

NEW FEATURES - singularity profile: * the profile has been simplified since the option '--containall' has been removed and the profile now sets 'autoMounts = true' * functionalities introduced in version 2.6.* to manage singularity bindings are not needed anymore * option 'params.containers.specificBinds' (used in the geniac-template) introduced in version-2.1.0 is not needed anymore * cmake option 'apmountdir' introduced in version-2.0.0 to bind folders inside containers is now deprecated since it is not needed anymore - Possibility to define label with variable: label (params.someValue ?: 'toolPrefix') - Geniac CLI: * 'geniac lint': improve error message when name of a conda recipe is not coherent with the label

- Python
Published by phupe about 3 years ago

https://github.com/bioinfo-pf-curie/geniac - version-2.6.3

version-2.6.3 01/06/2023

NEW FEATURES - singularity profile: * Allow the binding of relative (to launchDir) paths * Order the bindings according to the natural ordering - Geniac CLI: * Possibility to use 'geniac lint' on a repo even if the folder "geniac" is not present * 'geniac init': improve error message display

- Python
Published by phupe about 3 years ago

https://github.com/bioinfo-pf-curie/geniac - version-2.6.2

version-2.6.2 12/16/2022

NEW FEATURES - Geniac CLI * Conda env with apptainer 1.1.4

BUGFIX - singularity profile: * checkSymlink: avoid infinite loop in some limit conditions

- Python
Published by phupe over 3 years ago

https://github.com/bioinfo-pf-curie/geniac - version-2.6.1

version-2.6.1 12/07/2022

BUGFIX - singularity profile: * checkSamplePlan: conditions added to consider files with either 2, 3 or 4 columns

- Python
Published by phupe over 3 years ago

https://github.com/bioinfo-pf-curie/geniac - version-2.6.0

version-2.6.0 11/19/2022

NEW FEATURES -almalinux:8.7 set as default for the containers - singularity profile: * checkBindinds function takes into account the binding of possible symlink inside a path. It also binds the directory defined in 'params.outDir' if it is defined in the nextflow.config file.

BUGFIX - Geniac CLI: * 'geniac init' will throw an error if it is launched from the working directory to be created

- Python
Published by phupe over 3 years ago

https://github.com/bioinfo-pf-curie/geniac - version-2.5.0

version-2.5.0 08/04/2022

NEW FEATURES - Add support to apptainer - Upgrade tool versions for the geniac conda env - Check during the cmake configuration that mininal version for each software is met - Geniac CLI: * geniac lint adds an error message if conda recipe is not correctly formatted * geniac lint will ignore config file that are not explicitly declared in geniac.ini * when installing with sudo privilege, check that singularity and nextflow versions are the same as the one detected in the user environment during cmake configuration * avoid 'sudo' command with 'geniac install' if launched by the root user

BUGFIX - Geniac CLI: * Fix geniac lint error when comment in the middle of a line * geniac lint will throw an error if the withLabel process selector is single-line formatted in the process.config file * allow '.' in softName in the pip section of a conda recipe

DOCUMENTATION - Minimal conda version (4.12.0) required

- Python
Published by phupe almost 4 years ago

https://github.com/bioinfo-pf-curie/geniac - version-2.4.1

version-2.4.1 06/10/2022

NEW FEATURES - Geniac CLI: * allow both patterns ('condaChannelName::softName=version=buildString' and 'softName=version=buildString') in conda yml recipe file

- Python
Published by phupe about 4 years ago

https://github.com/bioinfo-pf-curie/geniac - version-2.4.0

version-2.4.0 06/08/2022

NEW FEATURES - conda 4.12.0 and almalinux:8.6 set as default for the containers - Geniac CLI: * check that conda recipe with a yml file contains an env name * check that conda recipe with a yml file have a unique env name * check that all dependencies with conda follow the pattern 'condaChannelName::softName=version=buildString' * check that pip dependencies with conda follow the pattern 'softName==version'

- Python
Published by phupe about 4 years ago

https://github.com/bioinfo-pf-curie/geniac - version-2.3.0

version-2.3.0 05/20/2022

NEW FEATURES - New cmake option: * apsingularitybuild_options: allow to pass specific options when building singularity images. - Geniac CLI: * singularityfakeroot mode added to "geniac install" - default runOption expected to "" in geniac.config - New profile available: podman

BUGFIX - Delete files generated by geniac when "geniac init" uses a path

DOCUMENTATION - Describe how to build singularity images with fakeroot option - Admin: explain how to build the doc

- Python
Published by phupe about 4 years ago

https://github.com/bioinfo-pf-curie/geniac - version-2.2.0

version-2.2.0 04/27/2022

NEW FEATURES - generate container recipes with renv and R tool - conda 4.11.0 and almalinux:8.5 set as default for the containers - Geniac CLI: * "clean", "configs" and "recipes" commands have been added * allow labels defined in params.geniac.tools in conf/geniac.config to use the content from other tools defined in params.geniac.tools * allow labels in params.geniac.containers.yum or params.geniac.containers.git scopes for all kind of labels (and not only for labels defined in params.geniac.tools) * check that the container recipes generated by geniac are not in the repo * allow custom scope in params.geniac.tools (which is required for a tool with R and renv) * geniac folder with the same version of geniac CLI is now included in the python package * add "sudo chown" after sudo operation to restore permission to the user * "geniac lint" now checks that a conda recipe must have its label in conf/geniac.config

- Python
Published by phupe about 4 years ago

https://github.com/bioinfo-pf-curie/geniac - version-2.1.0

version-2.1.0 03/24/2022

NEW FEATURES - Geniac CLI: * geniac folder with the same version of geniac CLI is downloaded in src dir to ensure that the pipeline will be installed using the same geniac version * config files generated by geniac are deleted at init if they are present in the src dir

DOCUMENTATION - option containers.specificBinds

- Python
Published by phupe over 4 years ago

https://github.com/bioinfo-pf-curie/geniac - version-2.0.1

version-2.0.1 03/18/2022

DOCUMENTATION - Update the config file examples generated by geniac

BUGFIX - Geniac CLI: allow the usage of --apsingularityimage_path

- Python
Published by phupe over 4 years ago

https://github.com/bioinfo-pf-curie/geniac - version-2.0.0

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/labelname (to allow the -resume option) - New cmake options: * aplinuxdistro and apcondarelease to bootstrap on containers available on 4geniac docker hub repositories (https://hub.docker.com/u/4geniac) * apmountdir 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: * options init, install, test, options have been added * available on PyPI (https://pypi.org/project/geniac) - 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 'buildconfig_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

- Python
Published by phupe over 4 years ago

https://github.com/bioinfo-pf-curie/geniac - version-1.1.0

version-1.1.0 08/09/2021

NEW FEATURES - Add retry errorStrategy in the nextflow.config - New cmake option apdockerregistry to bootstrap on custom registry when building the containers - baseDir replaced by projectDir - New method to detect is the source directory is a git repository

BUGFIX - Geniac linter supports empty recipes folder

DOCUMENTATION - Update the documentation and fix typos - Reference to the article added - Custom install section: add missing information where to save the custom recipes - Install from source code section: add missing link to modules/CMakeLists.txt template

- Python
Published by phupe over 4 years ago

https://github.com/bioinfo-pf-curie/geniac - version-1.0.0

version-1.0.0 31/05/2021

NEW FEATURES - Harmonization of docker.nf / singularity.nf files - Add missing indentation in singularity definition files