bio-tools-curation-tooling

The repo collect scripts and tools for aiding in the curation of new tools, e.g. coming from Pub2Tools and EdamMapper

Tutorials

The file workflow_tutorial.ipynb includes a detailed tutorial on how to implement the workflow after running Pub2Tools for a specific month (see Running Pub2Tools for one month. The workflow takes the output log from Pub2Tools, separate json files with low-priority tools and preprints as input (json files under folder data.

Pub2Tools

Installation

1. In your working directory, create a folder named "Pub2Tools".
2. Follow the installation guide at Install Pub2Tools.

Running Pub2Tools for one month

1. Create folder named month_year
2. Copy the following command and replace the folder name /work/Pub2Tools/MONTH_YEAR and month argument YYYY_MM

    java -jar -Xms2048M -Xmx4096M /work/Pub2Tools/pub2tools/target/pub2tools-cli-1.1.2-SNAPSHOT.jar -all /work/Pub2Tools/MONTH_YEAR --edam http://edamontology.org/EDAM.owl --idf https://github.com/edamontology/edammap/raw/master/doc/biotools.idf --idf-stemmed https://github.com/edamontology/edammap/raw/master/doc/biotools.stemmed.idf --month YYYY-MM --seleniumFirefox /work/Pub2tools/firefox/firefox/firefox-bin

Usually this takes 4-5 hours to finish.