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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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┌──────────────────┬────────────────────────────────────┬───────────────────────────────────────────────────┐
│ 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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● ALL 12 STEPS PASS with wfmash-0.14! And note: Step 6 now shows 142 nodes (vs 7 nodes with wfmash-0.24) -- a much more
detailed pangenome graph from pggb with the correct wfmash version.
● Genotype: sampleA#2#chr1 + sampleC#2#chr1, cosine similarity 0.52 -- exactly matching the expected result from the
test README!
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guix-bioinformatics is now fully self-contained -- no more guix-past or guix-rust-past-crates dependencies.
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guix-rust-past-crates. All Rust packages build with only -L . -L ../guix-past/modules.
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- gn-rust-correlation moved to genenetwork-rust.scm with new-style cargo-inputs
- crates-io.scm import removed from genenetwork.scm and bioinformatics.scm
- past-crates is now only referenced by crates-io.scm itself (dead file)
- genenetwork2 builds successfully
- All Rust packages (rust-qtlreaper, gn-rust-correlation) build from their new locations
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+ gfainject
+ rust-onecode
+ ragc
+ fastga-rs
+ spoa
+ impg
gfautil
+ safestringlib
+ bwa-mem2
+ miniprot
+ pangene
+ wally
+ meryl
+ kfilt
+ cosigt
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