galaxy-biotools-deb-toolinfo

Integration of tools information in Galaxy IUC Tools (primary) with Bio.tools and Debian Med

Authors

• Ivan Kuzmin @inkuzmin
• Matúš Kalaš @matuskalas

Contributors

• Hervé Ménager @rvmngr
• Galaxy and especially Galaxy IUC contributors (numerous, including Björn Grüning @bjoerngruening, Nicola Soranzo @NicolaSoranzo, etc.)
• Bio.tools curators and contributors (numerous, including Hans Ienasescu @HansIenasescu and Jon Ison)
• Debian Med contributors (of those especially Steffen Möller, Andreas Tille, @ssatta, Michael R. Crusoe @biocrusoe, etc.)
• get_doi function is based on the implementation of DOI fetcher by Kenzo-Hugo Hillion @khhillion

Based on previous work

• Adding tools annotation from Bio.tools into Galaxy IUC Tools by @inkuzmin (PR #1905 and #1897 in galaxyproject/tools-iuc)
• Retrieving tools annotation from Debian by @tillea (edam.sh in bio-tools/biotoolsConnect)
• Succession of integration efforts of tools information in Debian Med and Bio.tools by @smoe, @rvmngr, @matuskalas (bio-tools-community/debian-med-links-analysis, bio-tools-community/json-buffer, bio-tools-community/debian2biotools, archived toolinfowarehouse)

Licenses

Choice of MIT and CC-BY-4.0

Interactive report creation

Interactive report creation code consists of two parts:

1. A Jupyter notebook to find matches by DOI and generate JSON file with the data;
2. A client to display data in a browser in a form that facilitates the process of manual annotation of the Galaxy Tools with EDAM terms.

To start, explore, and rerun the notebook it is advisable to create a python3 virtual environment:

# create a virtual environment
$ python3 -m venv .venv

# activate the virtual environment
$ . .venv/bin/activate

# install Jupyter and start the notebooks server
$ pip install jupyter
$ jupyter notebook

# open the notebook in a browser: http://localhost:8888/notebooks/workflow.ipynb

# after all work is done to end the session:
(.venv)$ deactivate

To build the client:

# naviagate to the `client` folder with
$ cd client

# install dependencies
$ npm install

# serve with hot reload at localhost:8080
$ npm run dev

# build for production with minification and serve it with HTTP server
$ npm run build
$ cd dist
$ python -m SimpleHTTPServer 8000

TODO

• [] Annotate Galaxy instances (https://github.com/galaxyproject/galaxy-hub/tree/master/src/use)