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ToolFinder

Description

The purpose of ToolFinder is to present a landscape view of bioinformatics software packages & tools installed across Australian national computational infrastructures, including:

ToolFinder also:

  1. Presents relevant metadata for each of these tools, which is sourced from bio.tools,
  2. Provides connections to other global registries as appropriate, and based on user feedback (e.g. BioContainers), and
  3. Provides, where possible, the ability to directly access (or launch) bioinformatics tools. The only current example of this is for Galaxy Australia.

Diagram

How to cite this software

Add citation instructions here.

User guide

General build description

ToolFinder takes a curated list of bioinformatic software packages/tools, imports this list and uses a unique identifier to add metadata from bio.tools, and infrastructure specific tool information, for the above listed Australian national computational infrastructures.

For example, for Galaxy Australia this entails the tools available, and for the high performance computing infrastructures this entails the version(s) available for each software package.

It is recommended to use an IDE like pycharm to maintain and further develop ToolFinder.

Required (minimum) inputs / parameters

The essential steps required to rebuild ToolFinder are:

  1. A complete copy of this repository: https://github.com/AustralianBioCommons/australianbiocommons.github.io
  2. A series of minimum input files in the folder called external - these are listed in the Required (minimum) inputs/parameters section below

Note: some data is imported by interacting with an external API. This includes metadata from bio.tools, Galaxy Australia, and NCI.

Source Type Input(s) to ToolFinder Location? Curation required?
Australian BioCommons BioCommons Tool Matrix Matrix_of_Availability_of_Bioinformatics_Tools_across_BioCommons__deployment_version.xlsx external folder Yes
bio.tools Registry metadata https://bio.tools/api/t/ None - API Yes
Galaxy Australia Infrastructure API https://usegalaxy.org.au/api/tools None - API No
Australian BioCommons Galaxy Tools Matrix - used to match Galaxy tool IDs to Tool Matrix IDs galaxy_tools_curation.csv external folder Yes
NCI Infrastructure apps-service http://gadi-test-apps.nci.org.au:5000/dump None - API No
NCI Infrastructure apps-service for shared repository if89 http://130.56.246.237:5000/dump None - API No
NCI API key file gadi.key.hdr external folder No
NCI API key file for if89 bioapps_token.txt external folder No
Pawsey Infrastructure module list setonix.txt external folder No
QCIF / QRISCloud Infrastructure module list qriscloud.txt external folder No

Dependencies & third party tools

Install of the following is required to maintain and develop ToolFinder locally:

  • Python (3.8)
  • R (4.1.2)
  • pycharm (2021.2.3)

ToolFinder also depends on multiple APIs, including:

If any of these are changed, then this will also impact the operation of ToolFinder.

Additional notes

Any comment on major features being introduced, or default/API changes that might result in unexpected behaviours.

Help / FAQ / Troubleshooting

Tutorials

Please see these video tutorials available through the Australian BioCommons YouTube Channel:

License

Acknowledgements / citations / credits

This work is supported by the Australian BioCommons via funding from Bioplatforms Australia, the Australian Research Data Commons (https://doi.org/10.47486/PL105) and the Queensland Government RICF programme. Bioplatforms Australia and the Australian Research Data Commons are funded by the National Collaborative Research Infrastructure Strategy (NCRIS).

Tool metadata is sourced from bio.tools where possible

Ison, J. et al. (2015). Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research. DOI

bio.tools API

EDAM is used for tool list categorisation

Ison, J., Kalaš, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., Malone, J., Lopez, R., Pettifer, S. and Rice, P. 2013. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics, 29(10): 1325-1332. DOI PMID: 23479348 Open Access

EDAM ontology GitHub