Package: tooldirectory
ToolDirectoryIntroductionToolDirectory provides a convenient tool to display list of softwares in a webpage along with dynamic data filtering capabilities.You can test ourpublic demoDirect use of ToolDirectory ViewerToolDirectory is a Python 3.x program. It also requires the following package:requests >=2.25.1rich-click >=1.5.2loguru >=0.6.0conda create -p tooldir -c anaconda requests=2.25.1 rich-click=1.5.2 loguru=0.6.0Web rendering relies on the open-source version ofKeshifdata visualisation. We providedKatalog, a lightweight version specifically designed for ToolDirectory and DataDirectory.Basic usage$tooldir-hUsage:tooldir[OPTIONS]COMMAND[ARGS]...ToolDirectory:AdynamicvisualizationofpiecesofsoftwaremanagedbyaBioinformaticsCoreFacility╭─Options─────────────────────────────────────────────────────────────╮
│--versionShowtheversionandexit.│
│--help-hShowthismessageandexit.│
╰───────────────────────────────────────────────────────────────────────╯
╭─Mainusage──────────────────────────────────────────────────────────╮
│createCreatetoolpropertiesoraddanewversion│
│updateUpdatemetadataofatool│
│statusSetinstallationstatusofatool'sversion│
╰───────────────────────────────────────────────────────────────────────╯
╭─Visualization───────────────────────────────────────────────────────╮
│kcsvCreatecsvforKeshifvisualisation│
╰───────────────────────────────────────────────────────────────────────╯Data structureToolDirectory expects a directory structure with the following constraints:/path/to/tools/tool-name/tool-version/Or, withmodulesarchitecture:/path/to/tools/tool-name/modulefileOr, withmodulesarchitecture:<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
  .../...UsageCreation a tool descriptiontooldircreate-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 inBio.tools. You can manually fill the missing fields  but we strongly encourage you to create the tool description onBio.toolsand 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 metadatatooldirupdate-j/appli/bioinfo/spades/properties.jsonForce metadata search based on Bio.tools IDIt 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.tooldircreate-ninterproscan-v5.48-83.0-oacormier-binterproscan_ebitooldirupdate-j/appli/bioinfo/interproscan/properties.json-binterproscan_ebiSetup visualisationYou will needKatalog, a lightweight version ofKeshifspecifically designed for ToolDirectory and DataDirectory.gitclonehttps://gitlab.ifremer.fr/bioinfo/katalog.git/foo/bar/www/tooldirectoryThen, generate the software list:tooldirkcsv-p/path/to/tools/-c/foo/bar/www/tooldirectory/Softwares.csvYou can use a crontab to automatically update the software listing.LicensesTool Directory is released under the terms of the Apache 2 license.