nbipackager 0.0.3

A package manager for Singularity images

Packager

A command-line tool for managing Singularity images and creating executable bundles.

Installation

pip install .

Configuration

The configuration file is stored at ~/.config/packager.ini:

[packager]
singularity_path = /path/to/images
bin_path = /path/to/bin
packages_path = /path/to/packages

[images]
# This section is automatically populated by the tool

Usage

Add a set of singularity images

# From singularity_path
packager scanpackages
# From custom path
packager scanpackages --dir /qib/platforms/Informatics/transfer/outgoing/singularity/core

Add single singularity image as package

bashpackager addpackage --image /path/to/image.simg --name mypackage --version 1.0.0

Create a "HPC package" (bundle)

# Make an empty bundle
packager makebundle --name mybundle

# Make a bundle with one or more packages
packager makebundle --name denovo megahit=1.2.9 fastp=1.20.0

Add package to bundle

# By default each package is exposed as a binary called package. You can add "aliases" i.e. each binary to expose
packager addtobundle --name mybundle --package blast --version 1.0 blastn makeblastdb blastp