This repository lists the Singularity definition files and other files needed to deploy software on Bridges2 and similar systems maintained by the Pittsburgh Supercomputing Center.
| Category | Name | Latest | Last Commit | Container | Build ready | Publishing ready | TODO |
|---|---|---|---|---|---|---|---|
| Scientific tool | abyss | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | anvio | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | asciigenome | — | — | None | ❌ | ❌ | ☐ |
| Utility | asciinema | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | aspera-connect | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | augustus | — | — | None | ❌ | ❌ | ☐ |
| Utility | aws-cli | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | bamtools | v2.5.2 | 2026-06-18 | ✅ | ✅ | ✅ | ☑ |
| Utility | bat | v0.26.1 | 2026-05-12 | ✅ | ✅ | ❌ | ☐ |
| Scientific tool | bcftools | — | 2026-06-17 | None | ❌ | ✅ | ☐ |
| Scientific tool | bedops | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | bedtools | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | bioformats2raw | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | bismark | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | blast | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | blat | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | bowtie2 | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | braker2 | — | — | None | ❌ | ❌ | ☐ |
| Utility | browsh | — | 2026-05-11 | None | ✅ | ❌ | ☐ |
| Scientific tool | bsmap | — | — | None | ❌ | ❌ | ☐ |
| Utility | btop | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | busco | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | bwa | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | checkm | — | — | None | ❌ | ❌ | ☐ |
| Utility | circos | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | cutadapt | — | — | None | ❌ | ❌ | ☐ |
| Utility | cwltool | — | — | None | ❌ | ❌ | ☐ |
| Utility | dua | — | — | None | ❌ | ❌ | ☐ |
| Utility | dust | v1.2.4 | 2026-05-12 | ✅ | ✅ | ✅ | ☑ |
| Scientific tool | fastani | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | fastq-tools | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | fastqc | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | fasttree | — | — | None | ❌ | ❌ | ☐ |
| Utility | fdupes | — | — | None | ❌ | ❌ | ☐ |
| Utility | ffmpeg | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | filtlong | — | — | None | ❌ | ❌ | ☐ |
| Utility | flac | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | flash | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | funannotate | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | gatk | v4.6.2.0 | 2026-06-17 | ✅ | ✅ | ✅ | ☐ |
| Utility | gcalcli | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | genemark-es | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | gent | — | — | None | ❌ | ❌ | ☐ |
| Remote Desktop Application | gimp | — | — | None | ❌ | ❌ | ☐ |
| Utility | glances | — | — | None | ❌ | ❌ | ☐ |
| Utility | gnuplot | — | — | None | ❌ | ❌ | ☐ |
| Utility | graphviz | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | guppy | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | guppy-gpu | — | — | None | ❌ | ❌ | ☐ |
| Utility | hashdeep | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | hisat2 | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | hmmer | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | htslib | — | — | None | ❌ | ❌ | ☐ |
| Utility | hyperfine | — | — | None | ❌ | ❌ | ☐ |
| Utility | imagemagick | — | — | None | ❌ | ❌ | ☐ |
| Remote Desktop Application | inkscape | — | — | None | ❌ | ❌ | ☐ |
| Utility | jp | — | — | None | ❌ | ❌ | ☐ |
| Utility | jq | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | kraken2 | — | — | None | ❌ | ❌ | ☐ |
| Utility | lazygit | — | — | None | ❌ | ❌ | ☐ |
| Utility | libtiff-tools | — | — | None | ❌ | ❌ | ☐ |
| Utility | lowcharts | — | — | None | ❌ | ❌ | ☐ |
| Utility | mc | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | meme-suite | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | methylpy | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | nanoplot | — | — | None | ❌ | ❌ | ☐ |
| Utility | ncdu | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | ncview | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | octave | v11.1.0 | 2026-05-12 | ✅ | ✅ | ✅ | ☑ |
| Utility | pandiff | — | — | None | ❌ | ❌ | ☐ |
| Utility | pandoc | — | — | None | ❌ | ❌ | ☐ |
| Utility | papis | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | phylip-suite | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | picard | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | porechop | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | prodigal | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | raw2ometiff | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | raxml | — | — | None | ❌ | ❌ | ☐ |
| Utility | rclone | — | — | None | ❌ | ❌ | ☐ |
| Utility | rich-cli | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | rnaview | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | rust | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | salmon | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | samtools | — | — | None | ❌ | ❌ | ☐ |
| Utility | shellcheck | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | spades | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | sra-toolkit | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | star | v2.7.11b | 2026-06-18 | ✅ | ✅ | ✅ | ☐ |
| Scientific tool | star-fusion | v1.15.1 | 2026-06-17 | ✅ | ❌ | ✅ | ☐ |
| Scientific tool | stride | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | tiger | — | — | None | ❌ | ❌ | ☐ |
| Scientific tool | trimmomatic | v0.40 | 2026-06-17 | ✅ | ✅ | ❌ | ☐ |
| Scientific tool | vcf2maf | — | 2026-06-17 | None | ✅ | ❌ | ☐ |
| Scientific tool | viennarna | — | — | None | ❌ | ❌ | ☐ |
| Utility | vim | — | — | None | ❌ | ❌ | ☐ |
| Utility | visidata | v3.3 | 2026-05-12 | ✅ | ✅ | ✅ | ☑ |
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