QCIF is offering life sciences researchers across its Member institutions the ability to request that software modules be installed or updated on high-performance computing clusters accessed through QRIScloud, QCIF’s computing service.
The service is free for research staff and HDR students from QCIF’s Member institutions, including UQ, QUT, Griffith, JCU, CQU, UniSC, UniSQ and SCU.
Postdoctoral Research Fellow Dr Bree Tillett from The University of Queensland’s Frazer Institute, who is working towards causes and treatments of Type 1 diabetes, recently asked QCIF to install bioBakery 3 on UQ HPC Tinaroo as she had been unable to access the software. BioBakery 3 is one of the main pipelines that is used to analyse metagenomic sequencing and to identify strain-level bacterial changes.
“This has had a huge impact on my work,” said Bree. “I have many data sets that will be analysed using this pipeline. Without this pipeline, I am not able to analyse data sets to the standard that other university and research groups are producing, and would require collaborations to perform that data analyses.
“This pipeline will absolutely enable me to complete highly-publishable, in-depth analyses. It will also be beneficial to all labs that work on microbiome analyses, which is steadily growing.”
The installation of bioBakery turned out not to be straightforward, with QCIF Bioinformatician, Platform Developer and System Administrator Dr Justin Lee working with the pipeline’s developer to resolve issues.
“This resulted in a new release of the pipeline which brought it up to date with the required dependencies and newer databases,” said Peter Marendy, QCIF’s Head of Data Services.
Peter said QCIF used its software installation support to help more life sciences researchers, like Bree. “QCIF provides software installation support that allows researchers to request HPC-based software to be installed as required,” he said.
“QCIF’s HPC specialists work with the researchers to ensure that reliable, secure software and pipelines that meet the researcher’s needs are installed on the appropriate infrastructure. Advice on alternatives is also provided where HPC may not be the most appropriate option for the researcher’s computational needs.”
Before contacting QCIF with a software request, researchers should check what software is already installed on their HPC facility by using the ‘module avail’ command. The QCIF eResearch Analyst at your institution can assist you if required.
If the desired software is not already available, researchers may be able to install it themselves — please check our guide about how to do this.
If this is not possible, researchers should first contact their local eResearch team as, in some cases, they have permission to install software directly on a mandated HPC.
If the above three steps fail, QCIF Member researchers are very welcome to submit a software request via QCIF’s form.
The information provided will enable QCIF to identify the applicability of the requested tool across the life sciences community.