Galaxy Codex

Galaxy Communities Dock aka Galaxy Codex is a catalog of Galaxy resources (tools, training, workflows) that can be filtered for any community.

This repository stores the sources to build this catalog. The catalog is automatically updated every week.

The generated data of the catalog can be found in the dedicated results branch

Any Galaxy community can be added to this project and benefit from the dedicated resources, including interactive tables that can be embedded into subdomains and website via an iframe. Learn how to add your community in the dedicated GTN toturial.

Prepare environment

Install virtualenv (if not already there)

$ python3 -m pip install --user virtualenv

Create virtual environment
```
$ python3 -m venv env
```
Activate virtual environment
```
$ source env/bin/activate
```

Install requirements

$ python3 -m pip install -r requirements.txt

Extract Galaxy Tool Suites

This tool automatically collects a table of all available Galaxy tool suites including their metadata. Therefore, various sources are parsed to collect the metadata, such as:

GitHub (parsing each tool wrapper)
bio.tools
Bioconda
Galaxy server (availability, statistics)

The created table can be filtered to only show the tools relevant for a specific community.

The tool table benefits from EDAM annotations of the tools, this requires, that the tools are annotation via bio.tools. Learn how to improve metadata for Galaxy tools using the bio.tools registry.

Extract tool suites and filter per community automatically

A GitHub action performs every week the following steps:

Extract all tools by
1. Parsing tool GitHub repository from Planemo monitor listed
2. Checking in each repo, their .shed.yaml file and filter for categories, such as metagenomics
3. Extracting metadata from the .shed.yaml
4. Extracting the requirements in the macros or xml to get version supported in Galaxy
5. Checking available against conda version
6. Extracting bio.tools information if available in the macros or xml
7. Checking available on the 3 main galaxy instances (usegalaxy.eu, usegalaxy.org, usegalaxy.org.au)
8. Getting usage statistics form usegalaxy.eu
Create an interactive table for all tools: All tools
Filter the tool suite per community
Create an interactive table for all registered communities, e.g. microGalaxy

Extract all tools outside a GitHub Action

Get an API key (personal token) for GitHub
Export the GitHub API key as an environment variable:
```
$ export GITHUB_API_KEY=<your GitHub API key>
```
Run the script to extract all tools
```
$ bash bin/extract_all_tools.sh
```

The script will generate a TSV file with each tool found in the list of GitHub repositories and metadata for these tools:

Galaxy wrapper id
Description
bio.tool id
bio.tool name
bio.tool description
EDAM operation
EDAM topic
Status
Source
ToolShed categories
ToolShed id
Galaxy wrapper owner
Galaxy wrapper source
Galaxy wrapper version
Conda id
Conda version

Filter tools based on their categories in the ToolShed outside a GitHub Action

Run the extraction as explained before
(Optional) Create a text file with ToolShed categories for which tools need to be extracted: 1 ToolShed category per row (example for microbial data analysis)
(Optional) Create a TSV (tabular) file with tool status (1 tool suite per row) as 3 columns:
- ToolShed ids of tool suites (one per line)
- Boolean with True to keep and False to exclude
- Boolean with True if deprecated and False if not
Example for microbial data analysis

Run the tool extractor script

$ python bin/extract_galaxy_tools.py \
    filter \
    --all <Path to JSON file with all extracted tools> \
    --ts-filtered <Path to output TSV with tools filtered based on ToolShed category>
    --filtered <Path to output TSV with filtered tools based on ToolShed category and manual curation> \
    [--categories <Path to ToolShed category file>] \
    [--status <Path to a TSV file with tool status - 3 columns: ToolShed ids of tool suites, Boolean with True to keep and False to exclude, Boolean with True if deprecated and False if not>]

Training

Materials are extracted from the Galaxy Training Network and extended with information from Plausible (visits), YouTube (views), feedback and tools.

Extract training material and filter per community automatically

A GitHub action performs every week the following steps:

Extract all training by
1. Parsing the GTN API
2. Adding EDAM operations from the tools used in the tutorial
3. Adding visit stats using the Plausible API
4. Adding video view stats using YouTube API
5. Adding feedback from the GTN API
Create an interactive table for all tutorials
Filter the training per community based on tags
Create an interactive table for all registered communities

Extract tutorials from GTN outside a GitHub Action

Get an API key (personal token) for Plausible
Export the Plausible API key as an environment variable:
```
$ export PLAUSIBLE_API_KEY=<your GitHub API key>
```
Run the script
```
$ bash bin/extract_all_tutorials.sh
```

Filter tutorials based on tags outside a GitHub Action

Run the extraction as explained before
Create a file named tutorial_tags in your community data folder with the list of tutorial tags to keep

Run the following command

$ python bin/extract_gtn_tutorials.py \
    filter\
    --all "results/all_tutorials.json" \
    --filtered "results/<your community>/tutorials.tsv" \
    --tags "data/communities/<your community>/tutorial_tags"

Export

Generate wordcloud

Example to generate a wordcloud for the Galaxy tool suites with size of names of tool suites depends on the number of tool users in 2022-2023 on usegalaxy.eu:

$ python bin/create_wordcloud.py \
    --table "results/all_tools.tsv" \
    --name_col "Galaxy wrapper id" \
    --stat_col "No. of tool users (2022-2023) (usegalaxy.eu)" \
    --wordcloud_mask "data/usage_stats/wordcloud_mask.png" \
    --output "results/all_tools_wordcloud.png" \

Create interactive table in HTML

Example to generate an HTML file with an interactive table with microGalaxy tools that should be kept (True in To keep column)

$ python bin/create_interactive_table.py \
    --table "results/microgalaxy/tools.tsv" \
    --remove-col "Reviewed" \
    --remove-col "To keep" \
    --filter-col "To keep" \
    --template "data/interactive_table_template.html" \
    --output "results/microgalaxy/index.html"

Development

Tools

To make a test run of the tool to check its functionalities follow Usage to set-up the environnement and the API key, then run

Tool extraction
```
$ bash bin/extract_all_tools.sh test
```
This runs the tool, but only parses the test repository Galaxy-Tool-Metadata-Extractor-Test-Wrapper
Tool filter
```
$ bash bin/get_community_tools.sh test
```
Create interactive table and wordcloud
```
$ bash bin/format_tools.sh
```

Tutorials

Tutorial extraction

$ bash bin/extract_all_tutorials.sh test

Tutorial filtering

$ bash bin/get_community_tutorials.sh test

nsoranzo/galaxy_codex