Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/bioinfo-pf-curie/proteinfold-containers

https://github.com/bioinfo-pf-curie/proteinfold-containers

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: bioinfo-pf-curie
  • License: gpl-3.0
  • Language: Dockerfile
  • Default Branch: main
  • Size: 132 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 7
  • Releases: 0
Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

proteinfold-containers

This repository allows the build of docker container needed by the proteinfold pipeline. It builds the docker containers using GitHub Actions and pushes the containers on the 4geniac/proteinfold on Docker Hub.

We describe here how to add a new tool to the proteinfold pipeline.

Add a new tool

Create a git submodule with the tool version

For example, if you want to use the openfold version v2.1.0, you have to perform the following steps:

```

Add the tool as a git submodule

git submodule add https://github.com/aqlaboratory/openfold.git modules/openfold cd modules/openfold

Checkout the version you want to use

git checkout v.2.1.0

Push you modifications

cd ../.. git add modules/openfold .gitmodules git commit -m "[ADD] submodule OpenFold v.2.1.0 (Issue #1)" git push origin ```

Create the GitHub Actions workflow

Then, you have to define a workflow for the new tool. You can capilize on an exiting workflow:

cd .github/workflows cp alphafold3-base.yml openfold-base.yml

Edit the file openfold-base.yml and modify the following variables:

  • name
  • run-name
  • TOOL_NAME

Possibly, additional modification maybe required.

Commit and push the openfold-base.yml file.

Create and add the Dockerfile

You have to create the recipes/docker/openfold-v.2.1.0-base.Dockerfile. Use the following naming convention: TOOL_NAME-VERSION-base.Dockerfile.

Launch the GitHub actions

Connect on GitHub:

  • click on 'Actions'.
  • click on the workflow you want to launch
  • click on the button Run workflow, and again on the green button with the same name

Actions wkl

Actions run wkl

One completed, the openfold-v.2.1.0-base tag will be available in 4geniac/proteinfold on Docker Hub.

Owner

  • Name: Institut Curie, Bioinformatics Core Facility
  • Login: bioinfo-pf-curie
  • Kind: organization
  • Location: Paris, France

bioinformatics platform of the Institut Curie

GitHub Events

Total
  • Issues event: 10
  • Issue comment event: 2
  • Member event: 2
  • Push event: 67
  • Create event: 2
Last Year
  • Issues event: 10
  • Issue comment event: 2
  • Member event: 2
  • Push event: 67
  • Create event: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 8
  • Total pull requests: 0
  • Average time to close issues: about 1 month
  • Average time to close pull requests: N/A
  • Total issue authors: 3
  • Total pull request authors: 0
  • Average comments per issue: 0.25
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 8
  • Pull requests: 0
  • Average time to close issues: about 1 month
  • Average time to close pull requests: N/A
  • Issue authors: 3
  • Pull request authors: 0
  • Average comments per issue: 0.25
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • fredjarlier (4)
  • phupe (3)
  • QuentinDuvertCurie (1)
Pull Request Authors
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Dependencies

.github/workflows/alphafold-base.yml actions
  • actions/checkout v4 composite
  • docker/build-push-action v6 composite
  • docker/login-action v3 composite
  • docker/setup-buildx-action v3 composite