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ToolDirectory

Introduction

ToolDirectory provides a convenient tool to display list of softwares in a web page along with dynamic data filtering capabilities.

Tool Directory

You can test our public demo

Data visualization

Web rendering relies on Katalog viewer which simply expects you provide a ".csv" file containing the list of software metadata to use for visualization. The csv format expected by Katalog is quite simple, simply refer to this example to review column names (matadata).

Either you create that ".csv" file yourself (i.e. a dedicated script to collect software information installed on your cluster), of you use the Python ToolDirectory herafter presented.

Using ToolDirectory to manage bioinformatics softwares

Installation

ToolDirectory is a Python 3.x program. It also requires the following package:

  • requests >=2.25.1
  • rich-click >=1.5.2
  • loguru >=0.6.0
conda create -p tooldir -c anaconda requests=2.25.1 rich-click=1.5.2 loguru=0.6.0

Basic usage

$ tooldir -h
 Usage: tooldir [OPTIONS] COMMAND [ARGS]...                              
                                                                         
 ToolDirectory: A dynamic visualization of pieces of software managed by 
 a Bioinformatics Core Facility                                          
                                                                         
╭─ Options ─────────────────────────────────────────────────────────────╮
│ --version        Show the version and exit.                           │
│ --help     -h    Show this message and exit.                          │
╰───────────────────────────────────────────────────────────────────────╯
╭─ Main usage ──────────────────────────────────────────────────────────╮
│ create     Create tool properties or add a new version                │
│ update     Update metadata of a tool                                  │
│ status     Set installation status of a tool's version                │
╰───────────────────────────────────────────────────────────────────────╯
╭─ Visualization ───────────────────────────────────────────────────────╮
│ kcsv      Create csv for Keshif visualisation                         │
╰───────────────────────────────────────────────────────────────────────╯

Data structure

ToolDirectory expects a directory structure with the following constraints:

  • /path/to/tools/tool-name/tool-version/

Or, with modules architecture:

  • /path/to/tools/tool-name/modulefile

Or, with modules architecture:

  • <install-dir>/<tool>/

Here is an example:

/path/to/tools/
  ├── blast
  │    ├── 2.2.31 #Folder or modulefile
  │    └── 2.6.0
  ├── plast
  │    └── 2.3.2
  ├── beedeem
  │    └── 4.3.0
  .../...

Usage

Creation a tool description

tooldir create -n <tool-name> -v <tool-version> -o <username> -p /path/to/tools/

Sometimes the processus fails: it happens when the tool is not referenced yet in Bio.tools. You can manually fill the missing fields but we strongly encourage you to create the tool description on Bio.tools and recreate or update the json.

In the case of the installation of an addition of a new version, the json is modified to add the associated information without changing the metadata of the tool.

Update tool metadata

tooldir update -j /appli/bioinfo/spades/properties.json

Force metadata search based on Bio.tools ID

It may happen that the name you gave for the tool differs from the identifier given in Bio.tools. In this case, it is possible to force the search to retrieve the metadata.

tooldir create -n interproscan -v 5.48-83.0 -o acormier -b interproscan_ebi
tooldir update -j /appli/bioinfo/interproscan/properties.json -b interproscan_ebi

Setup visualisation

You will need Katalog viewer library.

git clone https://github.com/ifremer-bioinformatics/Katalog /foo/bar/www/ToolDirectory

Then, generate the software list:

tooldir kcsv -p /path/to/tools/ -c /foo/bar/www/ToolDirectory/Softwares.csv

You can use a crontab to automatically update the software listing.

Licenses

Tool Directory is released under the terms of the Apache 2 license.