Documentation for setting up a BioIT server.
This site covers the post install setup for a BioIT server based on Rocky Linux 8 or 9. Install the initial Rocky Linux 8 or 9 server with just the base packages and then follow the instructions on these pages to install a remote desktop and bioinformatics tools, as well as maintain up to date versions and add new tools to the platform.
To avoid using root, a build user will be created and the bioit github repository should be checked out into that user. The /opt/bioit location will also be owned by build.
Start at the Installation page.
Installation
Storage Setup
Slurm Cluster Setup
XFS User and Project Quotas
NFS User and Group Quotas
BioIT Repository
Services Setup
Updating
Applications
- abyss
- augustus
- bamtools
- bbmap
- bcftools
- bedtools2
- bismark
- bowtie
- bowtie2
- busco
- bwa
- chopper
- cutadapt
- dorado
- ea-utils
- FastQC
- fasttree
- gvcftools
- hisat2
- hmmer
- htslib
- igv
- longstitch
- mafft
- medaka
- minimap2
- multiqc
- nanoplot
- ncbi-blast
- nxtrim
- picard
- picrust2
- prokka
- R-core
- ragtag
- raven-assembler
- rtg-tools
- samtools
- seqkit
- SOAPdenovo2
- SolexaQA++
- stringtie
- tophat
- vcftools
- velvet
- vsearch