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- scripts/lib-pangenome-pack.sh — shared (sourced): resolves versions, builds the pack, writes md5sum.txt and the Markdown inventory. Exposes
pangenome_pack <fmt> <ext> <label> and pangenome_write_outputs.
- scripts/create-singularity-pangenome-tools.sh — 22 lines: sources the lib, calls pangenome_pack squashfs gz.squashfs singularity.
- scripts/create-docker-pangenome-tools.sh — 24 lines: sources the lib, calls pangenome_pack docker tar.gz docker.
md5sum.txt deduplicates by filename across runs and sorts by filename, so running both scripts produces a single combined manifest. The
inventory .md is identical content for both formats and names by <GBHASH>-<DATE> (no per-image hash, since contents are the same).
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- gn/packages/pangenome.scm:
- vg-1.71 (new): inherited from vg, pinned to v1.71.0.
- wfmash-0.14-snapshot (new): inherited from wfmash-0.14, pinned to commit 7bf8988. - pggb: inputs swap wfmash-0.14 → wfmash-0.14-snapshot. (Fixes the CIGAR skew everyone hit, not just
the workshop.)
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Added vg-1.71 to factory/guix-bioinformatics/gn/packages/pangenome.scm immediately after the existing vg
(v1.72.0). It inherits everything (build phases, native-inputs, inputs, synopsis, description, license,
properties) and only overrides version and source. The origin must repeat the snippet because
overriding source replaces the parent's whole origin record.
- Source: https://github.com/vgteam/vg/releases/download/v1.71.0/vg-v1.71.0.tar.gz
- sha256: 06ag9gb57wjvmxy4pzvskpkph6i6jvs0vy8rjm1xdk3g76l8vhjb
- guix package -A '^vg' now lists both vg 1.72.0 and vg 1.71.0.
- Workshop materials can pin via guix shell vg@1.71.0 or by referencing the vg-1.71 symbol directly from
a manifest.
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- gn/packages/pangenome.scm:
- vg-1.71 (new): inherited from vg, pinned to v1.71.0.
- wfmash-0.14-snapshot (new): inherited from wfmash-0.14, pinned to commit 7bf8988. - pggb: inputs swap wfmash-0.14 → wfmash-0.14-snapshot. (Fixes the CIGAR skew everyone hit, not just
the workshop.)
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Added vg-1.71 to factory/guix-bioinformatics/gn/packages/pangenome.scm immediately after the existing vg
(v1.72.0). It inherits everything (build phases, native-inputs, inputs, synopsis, description, license,
properties) and only overrides version and source. The origin must repeat the snippet because
overriding source replaces the parent's whole origin record.
- Source: https://github.com/vgteam/vg/releases/download/v1.71.0/vg-v1.71.0.tar.gz
- sha256: 06ag9gb57wjvmxy4pzvskpkph6i6jvs0vy8rjm1xdk3g76l8vhjb
- guix package -A '^vg' now lists both vg 1.72.0 and vg 1.71.0.
- Workshop materials can pin via guix shell vg@1.71.0 or by referencing the vg-1.71 symbol directly from
a manifest.
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The workshop tutorials and the pggb script use awk and which directly.
Add them to the meta-package so users get them in the same profile.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Drop recursive? #t, which fails in Guix sandbox (gettext.sh permission
denied during git submodule update). Add separate origin for zstr (not
in Guix) and link parallel-hashmap from Guix instead of bundled.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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three tables:
1. Pangenome tools -- 33 packages in the pangenomes meta-package
2. MEMPANG workshop -- additional R, Python, and utility packages
3. GeneNetwork packages -- 9 GN-specific packages
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┌──────────────────┬────────────────────────────────────┬───────────────────────────────────────────────────┐
│ Section │ Steps │ Result │
├──────────────────┼────────────────────────────────────┼───────────────────────────────────────────────────┤
│ vg construct │ vg construct -r tiny.fa -m 4 │ OK - creates graph │
├──────────────────┼────────────────────────────────────┼───────────────────────────────────────────────────┤
│ vg view + dot │ vg view -d ... | dot -T pdf │ OK - generates PDF │
├──────────────────┼────────────────────────────────────┼───────────────────────────────────────────────────┤
│ vg construct VCF │ vg construct -r ... -v tiny.vcf.gz │ OK │
├──────────────────┼────────────────────────────────────┼───────────────────────────────────────────────────┤
│ vg view paths │ vg view -dp / vg view -dpS │ OK │
├──────────────────┼────────────────────────────────────┼───────────────────────────────────────────────────┤
│ vg view GFA │ vg view + sed fix │ OK - GFA output correct │
├──────────────────┼────────────────────────────────────┼───────────────────────────────────────────────────┤
│ zgrep VCF │ zgrep '^##' -v | column -t │ OK │
├──────────────────┼────────────────────────────────────┼───────────────────────────────────────────────────┤
│ pggb DRB1-3123 │ pggb -i ... -n 12 -t 16 │ OK - graph: 21920bp, 4854 nodes, 12 paths │
├──────────────────┼────────────────────────────────────┼───────────────────────────────────────────────────┤
│ odgi stats │ odgi stats -S │ OK │
├──────────────────┼────────────────────────────────────┼───────────────────────────────────────────────────┤
│ pggb -p 95 │ underaligned graph │ OK - 55853bp, 62 nodes (confirms tutorial answer) │
└──────────────────┴────────────────────────────────────┴───────────────────────────────────────────────────┘
Two packages added to mempang-workshop: graphviz (for dot) and gzip (for zgrep).
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pangenomes
- tracepoints -- library-only Rust crate, already available as rust-tracepoints-0.1.0.66a5511 in pangenome-rust.scm
for dependency use; cigzip exposes its functionality as a CLI
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Including:
- pangenomes (meta-package: 28 pangenome tools)
- mempang-workshop (workshop meta-package: 20 direct + pangenomes)
- 27 other workshop-related and GeneNetwork packages
All test flag comments are in place, pafplot tests now run during build, and the manifest builds cleanly.
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The pangenomes meta package propagates:
wfmash, pggb, odgi, seqwish, smoothxg, impg, gfainject, gafpack, cosigt, minimap2, samtools, bedtools, bwa-mem2,
meryl, kfilt, miniprot, pangene, gfaffix, gfautil, vcfbub, wally, fastga-rs, htslib
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Rename manifest.scm to avoid guix pull compilation error [AI]
Replace local-file with git-fetch statements
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