Prioritized communication channel is on Microsoft Teams: BioinfoUgrp. Do not hesitate to use the ping function (putting @ and then the name, like in other chat systems), because the discussions on the Team app are a bit easy to miss otherwise.
Please "Google" the issues prior to contacting us. Very often, the main issues will already be reported and the solution available on the reference webpage of the program: in the Issues tab of GitHub for some, in GoogleGroups for others (e.g. for IQ-TREE). Other great platforms are StackOverflow, or Biostars.
Search with a keyword, for instance ml key clustal.
Execute ml bioinfo-ugrp-modules to make available the modules installed by the OIST Bioinfo user group. This line can be appended to your ~/.bashrc to make them available by default.
We autogenerate many modules from softwares packaged the Debian distribution. To see them, execute ml bioinfo-ugrp-modules DebianMed. More information is available on the DebianMedModules page.
To load a module in DebianMed (an example for loading bcftools):
# load DebianMed module first
ml bioinfo-ugrp-modules DebianMed
# now you can see the list of module installed in DebianMed.
ml avail
# load module
ml bcftools
# check the installation
bcftools --version
We provide some modules for Unix tools useful to everybody including bioinformaticians.
ml bioinfo-ugrp-modules UnixGoodies
ml av
Check oist/BioinfoUgrp_UnixGoodies_Images for details.
We have prepared a Nextflow module (ml bioinfo-ugrp-modules Nextflow2) and registered OIST's profile to the nf-core community so that you can run their pipelines with the -profile oist option on Deigo. A nf-core module is also available (ml bioinfo-ugrp-modules nf-core).
Under the Other/ namespace, we also provide some general bioinformatics tools such as:
- DIAMOND (
ml Other/DIAMOND/2.0.4.142) - InterProScan and its database (
ml Other/interproscan/5.48-83.0) - … and more !
See this page for the full list of modules and for more information.
Widely used databases were installed locally. Upon request by users, we plan on upgrading databases (not more than once a year). After upgrading a specific database, users will be asked if the older database should still remain available (completion of projects,...): it will be deleted after 30 days except if still required. At one time, a maximum of two versions of the same database will be available.
Check DataBases for details.
Here is how you can run RStudio on a compute node.
We have some modules on Saion for GPU-accelerated computations such that can not be run on Deigo. Please remember that the modules system on Saion is older, so the ml shortcuts will not work. To list the available modules, do:
module load bioinfo-ugrp-modules
module available
We have a basic module for AlphaFold 2.1.1. For a basic usage, you can do something similar to the example script in /bucket/BioinfoUgrp/alphafold/2.1.1/bin/alphafold_example_script.sh.
We have modules for basecalling Nanopore data, in particular for Guppy and Rerio.