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Container definitions for git-annex

Containerized versions of git-annex, for use when installing git-annex may be a bit more work than you'd like. This is expected to be especially useful on computer clusters, so we provide extra documentation for that use case.

This works by installing the git-annex standalone distribution inside of an Alpine Linux container.

Apptainer / Singularity

Apptainer (formerly Singularity is a container system especially designed for command line apps and/or HPC clusters. It emphasizes a good interface for running from the command line.

Download the latest raw image:

$ wget https://github.com/AaltoSciComp/git-annex-containers/releases/download/latest/git-annex.sif

Building from the docker image:

$ apptainer build git-annex.sif docker://ghcr.io/aaltoscicomp/git-annex:latest

The Dockerfile is the primary build (and that is how the released git-annex.sif is made). An old singularity definition file is included in case it is important for you:

$ apptainer build git-annex.sif git-annex.def

Running:

$ ./git-annex.sif [git-annex commands]

Apptainer usage tips

You can rename the .sif file to git-annex and put it in a directory on PATH, and then it will function exactly like the annex subcommand for your normal git installation: you can run git annex.

For use as a remote over SSH, you need to set up git-annex-shell. You can use git-annex.sif shell can be used, for example: git config remote.NAME.annex-shell "/path/to/git-annex.sif shell" Special cases that may occur:

  • If your repo is not in the default bind-mounted filesystems ($TMP, $HOME), you need to bind mount it. This can be used: git config remote.NAME.annex-shell "apptainer run -B /scratch /path/to/git-annex.sif shell"

On your own computer,this git-annex container can access your SSH authentication (keys, ControlMaster sockets). But there are some special cases:

  • To access your SSH agent, you need to bind the socket inside. You can export SINGULARITY_BIND=$SSH_AUTH_SOCK or run apptainer run -B $SSH_AUTH_SOCK git_annex.sif

  • git-annex sets up its own ControlMaster for mulitplexing. If you already have one running, set git config annex.sshcaching false it can automatically re-user existing ssh ControlMaster from /tmp, which is bind-mounted by default.

Docker

There's a Dockerfile here, but there may not be much use for it since the point of this repo is to run against local data, and docker isn't the ideal way to do that. Still, might be useful.

The Dockerfile is made mainly so that you can build Apptainer from docker by pulling the image (and this is the main way that Apptainer is build now).

$ docker pull ghcr.io/aaltoscicomp/git-annex:latest

Status

As of 2023, just created and seems to work. Improvements welcome (including usage tips)

See also