NAME

make_package - Install a "package" in the NBI HPC using a singularity image

VERSION

version 0.15.0

SYNOPSIS

make_package -i SINGULARITY_IMAGE [-p PACKAGE] COMMANDS...

DESCRIPTION

This script creates a package for running Singularity containers with specified commands. It creates a binary script that sets the necessary environment variables and launches Singularity with the provided container image.

NAME

make_package - Create package for installing Singularity containers as HPC packages

OPTIONS

-i, --image SINGULARITY_IMAGE

Specify the Singularity container image file to be used. Required.

-p, --package PACKAGE

Specify the package name. If not provided, the script will infer it from the image filename. It will be used as in source package PACKAGENAME.

-f, --force

Force overwriting existing binary or package path if they already exist.

COMMANDS

List of binaries shipping with the package, they will all be linked to the same launcher script. At least a "command" is required.

Note that images created from make_image_from_bioconda will have a list of binaries in /etc/binaries.txt, automatically used to create the links.

EXAMPLE

To install a package from a Singularity image called seqfu__1.20.0.simg with the binaries seqfu, fu-orf, fu-msa, fu-rename and fu-tabcheck:

make_package -i seqfu__1.20.0.simg seqfu fu-orf fu-msa fu-rename fu-tabcheck 

If the image was generated, you can simply:

make_package -i seqfu__1.20.0.simg

AUTHOR

Andrea Telatin <proch@cpan.org>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2023-2025 by Andrea Telatin.

This is free software, licensed under:

The MIT (X11) License