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Shared repository of tools and software (`project if89` on NCI)
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ABLeS participants have access to the Australian BioCommons Tools and Workflows project, in project allocation if89. This is a repository of popular tools, containers and workflows that can be used by anyone in the NCI user group. Anyone from an NCI users can contribute to if89 and add more tools that will be shared with others.

Software

The list of tools available through the Australian BioCommons Shared Tools and Workflows repository (NCI (if89)) is available through ToolFinder.

Utilising if89 tools

In order to load any modules from if89, you need to prepend the directory of if89's modules to the MODULEPATH environment variable using the following command:
module use -a /g/data/if89/apps/modulefiles
After that, you can load any tool, then utilising it directly using the following command:
module load $tool/$version
You can list all available modules using the following command:
module available

Contributing to if89 repository

Please see documentation for more information.

Containers

List of all available Containers

Will be available soon.

Workflows

List of all available Workflows

Will be available soon.

Software databases

Some of the databases required by different bioinformatics software tools are made available through the if89 project.
They are located at /g/data/if89/data_library. You can request other databases to be included by contacting us.

A list of the currently available (as of 25 Jan 2023) databases is included below:

List of all available databases

Dataset Source Download date Location Details
Blast Blast Webpage 28 Aug 2022 blast_db/28082022/ nr.*.gz: non-redundant protein sequence database with entries from GenPept, Swissprot, PIR, PDF, PDB, and RefSeq. nt.*.gz: nucleotide sequence database, with entries from all traditional divisions of GenBank, EMBL, and DDBJ.
Alphafold/UniProt foldseek github pages and AlphaFold Protein Structure Database webpage 30 Nov 2022 AlphaFoldDB/aminoacid/UniProt/30112022/ Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool.
Alphafold/UniProt-NO-CA foldseek github pages and AlphaFold Protein Structure Database webpage 30 Nov 2022 AlphaFoldDB/aminoacid/UniProt-NO-CA/30112022/ Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool.
Alphafold/UniProt50 foldseek github pages and AlphaFold Protein Structure Database webpage 30 Nov 2022 AlphaFoldDB/aminoacid/UniProt50/30112022/ Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool.
Alphafold/Proteome foldseek github pages and AlphaFold Protein Structure Database webpage 29 Nov 2022 AlphaFoldDB/aminoacid/Proteome/29112022/ Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool.
Alphafold/Swiss-Prot foldseek github pages and AlphaFold Protein Structure Database webpage 30 Nov 2022 AlphaFoldDB/aminoacid/Swiss-Prot/30112022/ Aminoacid dataset for foldseek tool. Downloaded through databases command in foldseek tool.
Busco/eukaryota_odb10 Busco webpages 14 Aug 2023 busco_db/14082023/lineages Lineage datasets for busco tool. Downloaded manually.


if89 Contributors

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