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README.md

singularityhub EMBL Rome

  1. Introduction
  2. Pulling
  3. Contributing

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.

Important: Since we do not have a premium account, I tried to find some workaround. We cannot secure completely that master will stay green. Please be careful to strictly follow the instructions.

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.

Important: Since we do not have a premium account, I tried to find some workaround. We cannot secure completely that master will stay green. Please be careful to strictly follow the instructions.

Important Bis: Each singularity should contain a single tool. Contact me ahead if you plan otherwise.

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/
  3. Position yourself on the "submission" branch: git checkout submission.
  4. Make sure that the content of the branch is up-to-date: git reset --hard main
  5. Add a singularity recipe inside recipes in the adapted folder.

Respect the naming format Singularity.toolName-tag (with a upper-case S). Please use common sense to choose the folder. If you are not sure, please contact me by email or by chat.

For instance, if you want to submit fastqc version 0119cv8, your file name will be Singularity.fastqc-0119cv8.

  1. Commit and push to the repository: `git add myrecipe && git commit -m "initial commit" && git push origin submission"
  2. Modify .gitlab-ci.yml in the "submission area" using the following template (replace toolName, tag, and path_to_recipe_folder):
toolName-tag-test:
  extends: .templateTest
  variables:
    BASENAME: toolName
    TAG: tag
    RECIPE_PATH: path_to_recipe_folder

For instance, if you want to submit fastqc version 0119cv8, your rule name will be fastqc-0119cv8-test and the path to the recipe /g/romebioinfo/tmp/singularityhub-emblrome/recipes/quality-control/fastqc.

  1. In the following instruction, please add toolName-tag-test` as a commit message.
  2. Push the file .gitlab-ci.yml to the repository: git add .gitlab-ci.yml && git commit -m "toolName-tag-test" && git push origin submission.
  3. Visit this page to submit a merge request.
  • As title: toolName-tag-test
  • description: A one-line sentence to explain what the tool is. Please precise any important information as well.
  • Reviewer: Choose Nicolas Descostes
  • Be careful: Uncheck the Delete source branch when merge request is accepted. before submitting.
  1. Now it is time to test the build of your singularity. You will see a gear on the right of Detached merge request pipeline #32160 waiting for manual action for . Click on it and hit the play button next to your rule.
  2. In the CI/CD > jobs (menu on the left), you can see your job running.
  3. Once your job passes the test (green checkmark), I will merge and deploy your singularity. I will let you know when this is done.