Singularity wrapper for MAGMA and LAVA software packages. Also includes ldblock software.
For LAVA, the example data is (https://github.com/josefin-werme/LAVA/tree/main/vignettes) is available within reference/example/lava folder. The folder also has a README file explaining how to trigger this analysis.
The ldblock tool (https://github.com/cadeleeuw/lava-partitioning) is also included in magma.sif container.
You may also have a look at unit-tests for a usage example.
Container files may get large and one should never add large binary files (.sif, .zip, .tar.gz, .mat, .dat, etc.) in git repositories directly, mainly files that can be parsed as raw text files (code files, etc.).
Git Large File Storage (LFS) should be used instead.
Before adding new files to this project after initialization (running python scripts/init.py), go through step 1-3 on the Git LFS homepage.
Revise the <magma>/.gitattributes file as necessary. Some common file formats has been added already.
magma- a hello-world introductory container setup
Below is the list of tools included in the different Dockerfile(s) and installer bash scripts for each container.
Please keep up to date (and update the main <magma>/README.md when pushing new container builds):
| OS/tool | Version | License | Source |
|---|---|---|---|
| ubuntu | 20.04 | Creative Commons CC-BY-SA version 3.0 UK licence | Ubuntu.com |
For instructions on how to build or rebuild containers using Docker and Singularity refer to <magma>/src/README.md.
Within this repository, the html-documentation can be built from source files put here using Sphinx. To do so, install Sphinx and some additional packages in python using Conda by issuing:
cd <magma>/docs/source
conda env create -f environment.yml # creates environment "sphinx"
conda activate sphinx # activates environment "sphinx
make html # builds html documentation into _build/html/ subdirectory
The built documentation can be viewed locally in a web browser by opening the file
<magma>/docs/source/_build/html/index.html
The documentation may also be hosted online on readthedocs.org.
If you face any issues, or if you need additional software, please let us know by creating a new issue.