A set of NGS singularity recipes, built for you and easily downlable
Project description
- Python version:
Python 3.7, 3.8, 3.9
- Source:
- Issues:
Please fill a report on github
- Platform:
This is currently only available for Linux distribution with bash shell (contributions are welcome to port the tool on MacOSX and other platforms)
Overview
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.
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.
Installation
If you are in a hurry, just type:
pip install damona --upgrade
and install Singularity.
Type damona in a shell. This will initiate the tool with a config file in your HOME/.config/damona directory and tell you to add this command in your .bashrc:
source ~/.config/damona/damona.sh
Open a new shell and you are ready to go. Please the Installation in details section for more information.
Quick Start
First create an environment called TEST:
damona env --create TEST
Second, activate it:
damona activate TEST
Third install some binaries/images:
damona install fastqc:0.11.9
That’s it. Time to test. Type fastqc.
To rename this TEST example:
damona env --rename TEST --new-name prod
or delete it:
damona env --delete prod
See more examples hereafter or in the user guide on https://damona.readthedocs.io
Motivation
As stated on their website, Conda 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 environments 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 communities have emerge using this framework. One of them is Bioconda, which is dedicated to bioinformatics.
Another great tool that emerged in the last years is Singularity. 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 other 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 singularity containers more easily.
Although it was start with the Sequana projet, 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 in details
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. 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:
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. Search the registry
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 searched for using:
damona search PATTERN
External registry can be set-up. For instance, the damona registry is accessible as follows:
damona search fastqc --url damona
Where damona is an alias defined in the .config/damona/damona.cfg that actullay looks 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. Activate an environment
damona activate base
4. install a Damona image
Download and install an image in your activate environment:
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/envs/base/bin directory.
To benefit from thoses binaries, you must change your PATH accordingly using:
export PATH=~/config/damona/bin:$PATH
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.
Changelog
Version |
Description |
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0.7.1 |
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0.7.0 |
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0.6.0 |
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0.5.3 |
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0.5.2 |
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0.5.1 |
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0.5.0 |
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0.4.3 |
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0.4.2 |
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0.4.1 |
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0.4.0 |
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0.3.X |
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0.3.0 |
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0.2.3 |
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0.2.2 |
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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 |
Project details
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