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| author | pjotrp | 2026-04-08 09:39:03 +0200 |
|---|---|---|
| committer | pjotrp | 2026-04-08 09:39:03 +0200 |
| commit | 184a67222d30510446c16efed016a369325ba46d (patch) | |
| tree | 349518bdf19afa004d62d426cb3e015d09ef2962 /gn | |
| parent | 195766c95fb9deec9d22d2eec2ac4a68edec3c90 (diff) | |
| download | guix-bioinformatics-184a67222d30510446c16efed016a369325ba46d.tar.gz | |
Fix cosigt propagation for workflow and missing getopts in pggb
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/pangenome.scm | 16 |
1 files changed, 16 insertions, 0 deletions
diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm index aa09df6..95afc2a 100644 --- a/gn/packages/pangenome.scm +++ b/gn/packages/pangenome.scm @@ -23,6 +23,7 @@ #:use-module (gnu packages cmake) #:use-module (gnu packages datastructures) #:use-module (gnu packages jemalloc) + #:use-module (gnu packages linux) #:use-module (gnu packages mpi) #:use-module (gnu packages algebra) #:use-module (gnu packages graph) @@ -409,6 +410,19 @@ unmapped reads using unique k-mers from pangenome graph alleles.") test))))))) (inputs (list go-github-com-akamensky-argparse go-gonum-org-v1-gonum)) + (propagated-inputs + (list bedtools + bwa-mem2 + gafpack + gfainject + htslib + impg + kfilt + meryl + minimap2 + odgi + pggb + samtools)) (home-page "https://github.com/pjotrp/cosigt") (synopsis "Cosine similarity-based structural haplotype genotyper") (description @@ -686,6 +700,7 @@ The path-guided stochastic gradient descent based 1D sort implemented in #$(this-package-input "seqwish") #$(this-package-input "smoothxg") #$(this-package-input "time") + #$(this-package-input "util-linux") #$(this-package-input "wfmash")))))) (list (string-append out "/bin/pggb") (string-append out "/bin/partition-before-pggb"))))))))) @@ -704,6 +719,7 @@ The path-guided stochastic gradient descent based 1D sort implemented in seqwish smoothxg time + util-linux wfmash-0.14)) (home-page "https://doi.org/10.1101/2023.04.05.535718") (synopsis "PanGenome Graph Builder") |