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 |
|---|---|---|---|---|---|---|
| Scientific tool | abyss | v2.1.5 | 2025-08-12 | ✅ | ✅ | ✅ |
| Scientific tool | anvio | v8 | 2025-08-19 | ❌ | ❌ | ✅ |
| Scientific tool | asciigenome | v1.17.0 | 2025-08-12 | ✅ | ✅ | ✅ |
| Utility | asciinema | v2.3.0 | 2025-08-12 | ✅ | ✅ | ✅ |
| Scientific tool | aspera-connect | v4.1.12 | 2025-08-12 | ✅ | ✅ | ✅ |
| Scientific tool | augustus | v3.5 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | aws-cli | v2.22.28 | 2025-08-12 | ✅ | ✅ | ✅ |
| Scientific tool | bamtools | v2.5.2 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | bat | v0.24.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | bcftools | v1.10.2 | 2025-08-12 | ✅ | ✅ | ✅ |
| Scientific tool | bedops | — | 2025-08-13 | None | ✅ | ✅ |
| Scientific tool | bedtools | v2.30.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | bioformats2raw | v0.9.4 | 2025-08-12 | ✅ | ✅ | ✅ |
| Scientific tool | bismark | — | 2025-08-13 | None | ✅ | ✅ |
| Scientific tool | blast | v2.13.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | blat | v36 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | bowtie2 | v2.4.4 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | braker2 | v2.1.6 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | browsh | — | 2025-08-13 | None | ✅ | ✅ |
| Scientific tool | bsmap | — | 2025-08-13 | None | ✅ | ✅ |
| Utility | btop | v1.0.20 | 2025-08-19 | ✅ | ✅ | ✅ |
| Scientific tool | busco | v5.2.2 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | bwa | v0.7.17a | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | checkm | v1.1.3 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | circos | v0.69-9 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | cutadapt | — | 2025-08-13 | None | ✅ | ✅ |
| Utility | cwltool | v3.1.20211020155521 | 2025-08-11 | ✅ | ✅ | ✅ |
| Utility | dua | v2.28.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | dust | v0.8.4 | 2025-08-19 | ✅ | ❌ | ✅ |
| Scientific tool | fastani | v1.3.3 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | fastq-tools | v0.8 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | fastqc | v0.12.1 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | fasttree | v2.1.11 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | fdupes | v2.4.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | ffmpeg | v7.1.1 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | filtlong | v0.2.1 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | flac | — | 2025-08-13 | None | ❌ | ✅ |
| Scientific tool | flash | — | 2025-08-13 | None | ✅ | ✅ |
| Scientific tool | funannotate | — | 2025-08-13 | None | ❌ | ✅ |
| Scientific tool | gatk | v4.2.0.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | gcalcli | v4.5.0 | 2025-08-12 | ✅ | ✅ | ✅ |
| Scientific tool | genemark-es | — | 2025-08-13 | None | ❌ | ✅ |
| Scientific tool | gent | v1.0.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Remote Desktop Application | gimp | v3.0.4 | 2025-08-09 | ✅ | ✅ | ✅ |
| Utility | glances | v3.3.1 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | gnuplot | v6.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | graphviz | v2.44.0 | 2025-08-13 | ✅ | ❌ | ✅ |
| Scientific tool | guppy | — | 2025-08-13 | None | ✅ | ✅ |
| Scientific tool | guppy-gpu | — | 2025-08-13 | None | ✅ | ✅ |
| Utility | hashdeep | v4.4 | 2025-08-13 | ✅ | ❌ | ✅ |
| Scientific tool | hisat2 | v2.2.1 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | hmmer | v3.3.1 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | htslib | v1.13 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | hyperfine | v1.17.0 | 2025-08-19 | ✅ | ✅ | ✅ |
| Utility | imagemagick | v7.1.1-39 | 2025-08-13 | ✅ | ✅ | ✅ |
| Remote Desktop Application | inkscape | v1.2.2 | 2025-08-10 | ✅ | ✅ | ✅ |
| Utility | jp | v0.2.1 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | jq | v1.7.1-r0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | kraken2 | — | 2025-08-13 | None | ✅ | ✅ |
| Utility | lazygit | v0.53.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | libtiff-tools | v4.2.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | lowcharts | v0.5.9 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | mc | v4.8.32 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | meme-suite | v5.4.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | methylpy | v1.4.3 | 2025-08-13 | ❌ | ✅ | ✅ |
| Scientific tool | nanoplot | v1.42.0 | 2025-08-19 | ✅ | ✅ | ✅ |
| Utility | ncdu | v2.8 | 2025-08-12 | ✅ | ✅ | ✅ |
| Scientific tool | ncview | v2.1.8 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | octave | v7.3.0 | 2025-08-13 | ✅ | ❌ | ✅ |
| Utility | pandiff | v0.6.0 | 2025-08-19 | ✅ | ✅ | ✅ |
| Utility | pandoc | v2.18 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | papis | — | 2025-08-19 | None | ❌ | ❌ |
| Scientific tool | phylip-suite | v3.697 | 2025-08-12 | ❌ | ✅ | ✅ |
| Scientific tool | picard | v2.23.2 | 2025-08-13 | ❌ | ✅ | ✅ |
| Scientific tool | porechop | v0.2.4 | 2025-08-13 | ✅ | ❌ | ✅ |
| Scientific tool | prodigal | v2.6.3 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | raw2ometiff | v3.0.0 | 2025-08-13 | ✅ | ❌ | ✅ |
| Scientific tool | raxml | v8.2.9 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | rclone | v1.70.3 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | rich-cli | v1.8.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | rnaview | v2.0.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | rust | v1.75.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | salmon | — | 2025-08-13 | None | ❌ | ✅ |
| Scientific tool | samtools | v1.21 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | shellcheck | v0.8 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | spades | v3.15.5 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | sra-toolkit | v2.11.0 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | star | v2.7.10b | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | star-fusion | v1.11.1 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | stride | v1995 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | tiger | v5.32.1-patch1 | 2025-08-12 | ✅ | ✅ | ✅ |
| Scientific tool | trimmomatic | 0.39 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | vcf2maf | v1.6.21 | 2025-08-13 | ✅ | ✅ | ✅ |
| Scientific tool | viennarna | v2.4.14 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | vim | v9.1 | 2025-08-12 | ✅ | ✅ | ✅ |
| Utility | visidata | v3.2 | 2025-08-13 | ✅ | ✅ | ✅ |
| Utility | wordgrinder | v0.8 | 2025-08-13 | ✅ | ✅ | ✅ |
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