Metadata-Version: 1.2
Name: damona
Version: 0.5.2
Summary: A set of NGS singularity recipes, built for you and easily downlable
Home-page: http://github.com/sequana/sequana
Author: Thomas Cokelaer
Author-email: thomas.cokelaer@pasteur.fr
Maintainer: Thomas Cokelaer
Maintainer-email: thomas.cokelaer@pasteur.fr
License: new BSD
Download-URL: https://github.com/sequana/sequana/archive/0.5.2.tar.gz
Description: DAMONA
        ######
        
        Damona is a singularity environment manager.
        
        Damona started as a small collections of singularity recipes to help installing third-party tools for
        `Sequana NGS pipelines <https://sequana.readthedocs.io>`_.
        
        Damona is now used to create environments where singularity images and their associated binaries can be installed altogether.
        
        In a nutshell, Damona combines the logic of Conda environments with the
        reproducibility of singularity containers. We believe that it could be useful for
        other projects and therefore decided to release it as an independent tool.
        
        .. image:: https://badge.fury.io/py/damona.svg
            :target: https://pypi.python.org/pypi/damona
        
        
        .. image:: https://github.com/cokelaer/damona/actions/workflows/ci.yml/badge.svg
           :target: https://github.com/cokelaer/damona/actions/workflows/ci.yml
        
        .. image:: https://coveralls.io/repos/github/cokelaer/damona/badge.svg?branch=master
            :target: https://coveralls.io/github/cokelaer/damona?branch=master
        
        .. image:: http://readthedocs.org/projects/damona/badge/?version=latest
            :target: http://damona.readthedocs.org/en/latest/?badge=latest
            :alt: Documentation Status
        
        .. image:: https://zenodo.org/badge/282275608.svg
           :target: https://zenodo.org/badge/latestdoi/282275608
        
        
        :Python version: Python 3.6, 3.7, 3.8
        :Source: See  `http://github.com/cokelaer/damona <https://github.com/cokelaer/damona/>`__.
        :Issues: Please fill a report on `github <https://github.com/cokelaer/damona/issues>`__
        :Platform: This is currently only available for Linux distribution with bash shell (contributions are welcome to port the tool on MacOSX and other platforms)
        
        
        Motivation
        ==========
        
        As stated on their website, `Conda <https:/docs.conda.io/en/latest>`_ is
        an open source **package** management system
        and **environment** management system.
        Conda provides pre-compiled releases of software; they can be installed in
        different local environment that do not interfer with your system. This has
        great advantages for developers. For example, you can install a pre-compiled
        libraries in a minute instead of trying to compile it yourself including all
        dependencies. Different community have emerge using this
        framework. One of them is `Bioconda <https://bioconda.github.io>`_, which is dedicated to bioinformatics.
        
        Another great tool that emerged in the last years is
        `Singularity <https://sylabs.io/docs>`_. Singularity containers can be used
        to package entire scientific workflows,
        software and libraries, and even data. It is a simple file that can be shared
        between environments and guarantee exectution and reproducibility.
        
        Originally, Conda provided pre-compiled version of a software. Nowadays, it also provides
        a docker and a singularity image of the tool. On the othe side, Singularity can include an
        entire conda environment. As you can see everything is there to build reproducible tools and
        environment.
        
        Now, what about a software in development that depends on third-party packages ? 
        You would create a conda environment and starts installing the required packages.
        Quickly, you will install another package that will break your environment due
        to unresolved conlicts; this is not common but it happens. In the worst case
        scenario, the environment is broken. In facilities where users depends on you,
        it can be quite stresful and time-consuming to maintain several such
        environments. This is why we have moved little by little to a very light conda
        environment where known-to-cause-problem packages have been shipped into
        singularity containers. This means we have to create aliases to those
        singularities. The singularities can be simple executable containers or full
        environment containers with many executables inside. In both cases, one need to
        manage those containers for different users, pipelines, versions etc. This
        started to be cumbersome to have containers in different places and update
        script that generate the aliases to those executables.
        
        
        That's where **damona** started: we wanted to combine the conda-like environment framework to manage our singularitiy containers more easily.
        
        Our goal is not to replace existing registry of biocontainers such as
        biocontainers but to use existing images, download them and manage them locally.
        Although **Damona** has some recipes and images (on
        sylabs/cokelaer/damona dn https://biomics.pasteur.fr/drylab/damona), those
        containers are for testing and help managing and installing the third-party
        tools required by `Sequana <sequana.readthedocs.io>`_ pipelines.
        
        We will therefore maintain damona in the context of Sequana project. Yet,
        **Damona** may be useful for others developers who wish to have a quick and easy
        solution for their users when they need to install third-party libraries.
        
        Before showing real-case examples, let us install the software itself.
        
        
        Installation
        ============
        
        The is the egg and chicken paradox. To get reproducible container with
        singularity, at some point you need to install singularity itself. That the first
        of the two software that you will need to install. Instructions
        are on `singularity web site <https://sylabs.io/guides/3.6/user-guide/>`_. This
        is not obvious to be honest. You need the GO language to be installed as well. I
        personally installed from source and it worked like a charm.
        
        Second, you need **Damona**. This is a pure Python sotfware with only a few
        dependencies. Install it with the **pip** software provided with your Python
        installation (Python 3.X)::
        
            pip install damona --upgrade
        
        Type **damona** to create the Damona tree structure. Images and binaries 
        will be saved in your home directory within the
        ~/.config/damona directory. There, two special files should be available:
        **damona.sh** and **damona.cfg**. Check that those files are present.
        
        Finally, you need to tell your system where to find damona. For bashrc users,
        please add those two lines to you bashrc file::
        
            export DAMONA_EXE="PATH_TO_DAMONA_BINARY"
            source ~/.config/damona/damona.sh
        
        open a new shell and type **damona** and you should be ready to go.
        
        Quick Start
        ============
        
        1. *list* available environments
        --------------------------------
        
        By default you have an environment called **base**. You can check the list of
        environment and their contents at any time using::
        
            damona env
        
        2. list installed images and binaries
        -------------------------------------
        
        You can get the binaries installed in an environment (and the images used by
        them)::
        
            damona info base
        
        3. See what is available
        ------------------------
        
        By default, we provide some recipes (for testing mostly but also to complement existing
        registries when a tool is missing) and their images. They can be listed as
        follows::
        
            damona available-images
        
        External registry can be setup. For instance, the damona registry is accessible
        as follows::
        
            damona available-images --url damona
        
        Where *damona* is an alias defined in the .config/damona/damona.cfg that
        actullay look for https://biomics.pasteur.fr/drylab/damona/registry.txt
        
        You may retrieve images from a website where a registry exists (see the developer
        guide to create a registry yourself).
        
        4. *install* a Damona image
        ----------------------------
        
        Download the one you want to use::
        
            damona install fastqc:0.11.9
        
        This will download the container in your ./config/damona/images directory and create an
        executable for you in ~/.config/damona/bin.
        
        This is your *base* environment. All images are stored in this directory
        *~/.config/damona/images*. By default binaries are stored in the *~./config/damona/bin* directory.
        
        To benefit from thoses binaries, you must change your PATH accordingly using::
        
            export PATH=~/config/damona/bin:$PATH
        
        or use the **activate** command explained hereafter, which is more convenient.
        
        
        5. **activate/deactivate** command
        ----------------------------------
        
        You can change your PATH environment on the fly to use one or several
        environments. However, we provide a more convenient mechanism based on **conda** commands. If you want to used your based environment, you can simply activate it using::
        
            damona activate base
        
        Once done, you can quit the shell or deactivate your environment specically
        using its name ::
        
            damona deactivate base
        
        or if you just wish to deactivate the last environment that you have activated::
        
            damona deactivate
        
        You can call this commands several times until no more **damona** environments
        are active.
        
        3. combine two different environments
        --------------------------------------
        
        In damona, you can have sereral environments in parallel and later activate the
        ones you wish to use. Let us create a new one::
        
            damone env --create test1
        
        and check that you now have one more environment::
        
            damona env
        
        We want to create an alias to the previously downloaded image of fastqc tool but
        in the *test1* environment. First we activate the newly create environment::
        
            damona activate test1
        
        then, we install the container::
        
            damona install fastqc:0.11.9
        
        This will not download the image again. It will just create a binary in the
        ~/.config/damona/envs/test1/bin directory.
        
        you can combine this new environemnt with the base one::
        
            damona activate base
        
        If you are interested to know more, please see the User Guide and Developer
        guide here below.
        
        Roadmap
        =======
        
        **Damona** is pretty new but here is short roadmap
        
        * do we store all images in the damona/images or do we store them in individual
          environement (with possible duplicates).
        * when installing a binaries from image A, then from image B. If we now delete image B.
          The binary is broken where image A could support this binary ! we should have a
          mechanism that handle this feature to recover the binary from other installed
          images. Like a history.
        * keep a version in damona.sh to allow a smooth/transparent update ?
        * check for registry not synchrone with github or shall we download the registry
          from github ? 
        
        Changelog
        =========
        
        ========= ====================================================================
        Version   Description
        ========= ====================================================================
        0.5.2     * add missing shell package
        0.5.1     * add DAMONA_SINGULARITY_OPTIONS env variable in the binary
                  * Fix the way binaries are found in the releases.
                  * new recipes: rtools
                  * new releases: sequana_tools_0.10.0
                  * Fix shell script to handle DAMONA_EXE variable 
        0.5.0     * Major refactoring. 
        
                    - Simplification of the registries (dropping notion of exe/set 
                      class
                    - Main script should now be fully functional with functional
                      activation/deactivation. 
                    - New command to build images from local recipes or dockerhub 
                      entries.
                    - Install command can now install local container. 
                    - DAMONA_PATH can be set to install damona images/binaries 
                      anywhere, not just in local home. 
                    - check md5 of images to not download/copy again
        0.4.3     * Implement damona activate/deactivate
        0.4.2     * Fix typo in the creation of aliases for 'set' containers
        0.4.1     * implemented aliases for the --from-url option stored in a
                    damona.cfg file
        0.4.0     * implemented the 'env' and 'activate' command
                  * ability to setup an external registry on any https and retrieve
                    registry from there to download external images
        0.3.X     * add gffread, rnadiff recipes
        0.3.0     * A stable version with documentation and >95% coverage read-yto-use
        0.2.3     * add new recipes (rnadiff)
        0.2.2     * Download latest if no version provided
                  * include *build* command to build image locally
        0.2.1     fixed manifest
        0.2.0     first working version of damona to pull image locally with binaries
        0.1.1     small update to fix RTD, travis, coveralls
        0.1       first release to test feasibility of the project
        ========= ====================================================================
        
        
        
        
        
        
        
        
        
        
        
Keywords: NGS,singularity
Platform: Linux
Platform: Unix
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
