icaoberg/List of Singularity Containers

Created Wed, 25 Aug 2021 22:05:41 +0000 Modified Wed, 25 Aug 2021 22:05:41 +0000

This summer, I was able to secure funding through XSEDE for an intern. Hind Albakri joined the Biomedical Applications Group to help me migrate, test and build Singularity containers to deploy applications to Bridges-2.

This happened for two reasons,

  1. I personally prefer to deploy every app as a container and
  2. I needed to design a procedure to deploy and make them public for the benefit of our users and community.

I am very happy with the outcome, since

  1. the repos have been migrated,
  2. documentation was written for the benefit of power users and staff members at PSC, and
  3. a procedure was designed and implemented for future deployments.

Here is a list of the repositories for the packages that have been prepared to be deployed or have been deployed to Bridges-2.


Name Information
abyss StatusStatusLicense
asciigenome StatusStatusLicense
aspera-connect StatusStatusLicense
bamtools StatusStatusLicense
bcftools StatusStatusLicense
bedtools StatusStatusLicense
bismark StatusStatusLicense
blast StatusStatusLicense
bowtie2 StatusStatusLicense
busco StatusStatusLicense
bwa StatusStatusLicense
cutadapt StatusStatusLicense
fastani StatusStatusLicense
fastqc StatusStatusLicense
fasttree StatusStatusLicense
gatk StatusStatusLicense
gent StatusStatusLicense
hisat2 StatusStatusLicense
hmmer StatusStatusLicense
htslib StatusStatusLicense
kraken2 StatusStatusLicense
methylpy StatusStatusLicense
ncview StatusStatusLicense
octave StatusStatusLicense
phylip-suite StatusStatusLicense
picard StatusStatusLicense
prodigal StatusStatusLicense
raxml StatusStatusLicense
salmon StatusStatusLicense
samtools StatusStatusLicense
spades StatusStatusLicense
spades StatusStatusLicense
sra-toolkit StatusStatusLicense
star StatusStatusLicense
tiger StatusStatusLicense
trimmomatic StatusStatusLicense
trimmomatic StatusStatusLicense
vcf2maf StatusStatusLicense
viennarna StatusStatusLicense


Name Information
asciinema StatusStatusLicense
aws-cli StatusStatusLicense
bat StatusStatusLicense
browsh StatusStatusLicense
dust StatusStatusLicense
fdupes StatusStatusLicense
ffmpeg StatusStatusLicense
flac StatusStatusLicense
gnuplot StatusStatusLicense
graphviz StatusStatusLicense
hyperfine StatusStatusLicense
imagemagick StatusStatusLicense
lazygit StatusStatusLicense
mc StatusStatusLicense
ncdu StatusStatusLicense
octave StatusStatusLicense
pandoc StatusStatusLicense
rclone StatusStatusLicense
visidata StatusStatusLicense