Register Apps

👾 Register versioned toil container pipelines, singularity containers, and python packages.

Installation

This package is available at PyPi:

pip install register_apps
# or with the latest version
pip install git+https://github.com/papaemmelab/register_apps.git#egg=register_apps

Usage

This package it's used to register versionized and containerized applications within a production environment. It provides 3 commands:

• 🍡 register_toil
• 📦 register_singularity
• 🐍 register_python

⚠️ WARNING: This package only works with singularity 2.4+

Register a toil containerized application

• 🍡 register_toil will install toil container pipelines in separate virtual environments, pull a singularity image from the dockerhub and create executables that call the pipeline with the right parameters:

    register_toil \
        --pypi_name toil_disambiguate \
        --pypi_version v0.1.2 \
        --bindir /example/bin \
        --optdir /example/opt \
        --tmpvar $TMP \
        --volumes /ifs /ifs
  

  Given this call, the following directory structure is created:

    /example/
    ├── bin
    │   └── toil_disambiguate_v0.1.2 -> /example/opt/toil_disambiguate/v0.1.2/toil_disambiguate
    └── opt
        └── toil_disambiguate
            └── v0.1.2
                ├── toil_disambiguate
                └── toil_disambiguate-v0.1.2.simg
  

  And the executables look like this:

    cat /example/bin/toil_disambiguate
    #!/bin/bash
    /path/to/.virtualenvs/production__toil_disambiguate__v0.1.2/bin/toil_disambiguate $@ \
        --singularity /example/opt/toil_disambiguate/v0.1.2/toil_disambiguate-v0.1.2.simg \
        --volumes /ifs /ifs \
        --workDir $TMP_DIR
  

• 📦 register_singularity provides a similar usage to register regular commands that will run inside a container, it will create the same directory structure but the executables created will execute commands inside the container:

    register_singularity \
        --target svaba \
        --command svaba \
        --image_url docker://papaemmelab/docker-svaba:v1.0.0 \
        --bindir /example/bin \
        --optdir /example/opt \
        --tmpvar $TMP \
        --volumes /ifs /ifs
  

  Given this call, the following directory structure is created:

    /example/
    ├── bin
    │   └── svaba -> /example/opt/docker-svaba/v1.0.0/svaba
    └── opt
        └── docker_svaba
            └── v1.0.0
                ├── svaba
                └── docker-svaba-v1.0.0
  

  And the executables look like this:

    cat /example/bin/svaba
    #!/bin/bash
    singularity exec \
        --workdir $TMP_DIR/${USER}_docker-svaba_v1.0.0_`uuidgen` \
        --pwd `pwd` \
        --bind /ifs:/ifs \
        /example/opt/docker-svaba/v1.0.0/docker-svaba-v1.0.0.simg svaba "$@"
  

• 🐍 register_python provides a method to register python packages without registering to run inside a container. It will create a similiar versionized directory structure and installing the python package and its dependencies within a virtual environemnt:

    register_python \
        --pypi_name click_annotvcf \
        --pypi_version v1.0.7
        --bindir /example/bin \
        --optdir /example/opt
  

  Given this call, the following directory structure is created:

    /example/
    ├── bin
    │   └── click_annotvcf_v1.0.7 -> /example/opt/click_annotvcfs/v1.0.7/click_annotvcf
    └── opt
        └── click_annotvcf
            └── v1.0.7
                └── click_annotvcf
  

  And the executables look like this:

    cat /example/bin/click_annotvcf_v1.0.7
    #!/bin/bash
    /path/to/.virtualenvs/production__click_annotvcf__v1.0.7/bin/click_annotvcf "$@"
  

Environment Variables

Some default values can be set using environment variables:

Variable	Default value for	Description	Example
REGISTER_APPS_BIN	--bindir	Path to the directory where the executables symlinks will be created	i.e. /apps/local/bin
REGISTER_APPS_OPT	--optdir	Path to the directory where the containers and scripts will be installed	i.e. /apps/opt
REGISTER_APPS_VOLUMES	--volumes	Comma-separated volumes in the format {src}:{dst} or just {src}	i.e. /mnt/data,/scratch,/usr/local/data:/data will mount in docker as -v /mnt/data:/mnt/data -v /scratch:/scratch -v /usr/local/data:/data.

Contributing

Contributions are welcome, and they are greatly appreciated, check our contributing guidelines!

Credits

This package was created using Cookiecutter and the papaemmelab/cookiecutter-toil project template.