List of Singularity definition files, modulefiles and more

This repository lists the Singularity definition files and other files needed to deploy software on Bridges2, HuBMAP HIVE and Brain Image Library.

STEM

Name	Information
abyss
anvio
asciigenome
aspera-connect
augustus
bamtools
bcftools
bedops
bedtools
bioformats2raw
bismark
blast
blat
bowtie2
braker2
bsmap
busco
bwa
checkm
cutadapt
fastani
fastq-tools
fastqc
fasttree
filtlong
flash
funannotate
gatk
genemark-es
gent
guppy
guppy-gpu
hisat2
hmmer
htslib
kraken2
meme-suite
methylpy
nanoplot
ncview
octave
phylip-suite
picard
porechop
prodigal
raw2ometiff
raxml
rnaview
rust
salmon
samtools
spades
sra-toolkit
star
star-fusion
tiger
trimmomatic
vcf2maf
viennarna

Utilities

Name	Information
asciinema
aws-cli
bat
browsh
btop
circos
cwltool
dua
dust
fdupes
ffmpeg
flac
glances
gnuplot
graphviz
hashdeep
hyperfine
imagemagick
jp
jq
lazygit
libtiff-tools
lowcharts
mc
ncdu
octave
pandiff
pandoc
rclone
rich-cli
shellcheck
vim
visidata
wordgrinder

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The Biomedical Applications Group at the Pittsburgh Supercomputing Center in the Mellon College of Science at Carnegie Mellon University.