Applications
Each application is listed here with the necessary instructions to build it from source.
Note that all tools go into the /opt/bioit directory followed by their name and then versions for each. This way we can keep all versions of tools available. By default RPMs are built that set the alternatives for each tool to the latest version so users will always have the best version but they can also use the environment modules to choose another version.
List of applications and instructions on building them
- 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