singularityhub EMBL Rome

1. Introduction
2. Pulling
3. Contributing
   • Testing your singularity beforehand
     • In Local
     • on gitlab
   • Adding to repository
4. Style guidelines
   • Singularity recipe
   • gitlab ci yml

Introduction

This repository aims at sharing singularity images among the EMBL community. We try to follow a strict model to provide uniformly designed singularities. Please let us know if we should modify anything.

Pulling

Please read the entire section before trying to pull any singularities.

To pull an existing singularity, first have a look at the image of interest in the list here or in this folder.

Copy the script below in a download.sh file and run the command: bash dowload.sh username containername imagename. For example, bash download.sh descoste fastqcv0019.sif 'fastqc:0119'.

#!/usr/bin/bash

USERNAME=$1
CONTAINERNAME=$2
IMAGE=$3

singularity pull --docker-username $USERNAME --docker-password $SINGULARITY_DOCKER_PASSWORD $CONTAINERNAME oras://git.embl.de:4567/descoste/singularityhub-emblrome/$IMAGE

Important: You need to define a git token to be able to use the $SINGULARITY_DOCKER_PASSWORD variable. Follow these steps:

1. Click on your avatar at the top right of your gitlab page.
2. Click on preferences.
3. Click on Access Tokens.
4. Enter a Token name. ex: "singularitypull".
5. In the Select scopes section, select read_registry.
6. Click Create personal access token.
7. At the beginning of the new loaded page, click on the folder icon to copy your new personal access token.
8. Edit your .bashrc (emacs -nw ~/.bashrc or vim ~/.bashrc) by adding export SINGULARITY_DOCKER_PASSWORD="paste_your_copied_access_token_here" wherever you like.
9. After closing your editor, run exec bash.
10. Now try to pull a particular singularity following the instructions above.

Contributing

This repository is maintained by Nicolas Descostes and Francesco Tabaro. To add a new singularity recipe, you need to:

1. Clone the repository: git clone git@git.embl.de:descoste/singularityhub-emblrome.git
2. Enter the folder: cd singularityhub-emblrome/

In order to test your singularity, you need to redirect the repository to one of your own:

3. Go to gitlab and create a new project: 'test-singularity' (**Unselect 'Initialize repository with a README')
4. In the singularityhub-emblrome/, enter git remote -v. You should see:

origin  git@git.embl.de:descoste/singularityhub-emblrome.git (fetch)
origin  git@git.embl.de:descoste/singularityhub-emblrome.git (push)

5. Set the new URL as the new target. You can find the new URL under the 'clone' button on gitlab. Copy the ssh address and run git remote set-url origin mynewurl. For instance git remote set-url origin git@git.embl.de:descoste/test-singularity.git.
6. Check that your repository targets the correct URL by running again git remote -v.
7. push the whole repository to the new location:

git add .
git push