From e45cfef8875c7151de8d03db0dcc8e22374d01b0 Mon Sep 17 00:00:00 2001 From: Richard Burhans Date: Tue, 1 Sep 2026 11:58:00 -0400 Subject: [PATCH] Add seven two-package combinations for the BRC pangenome tool set Each of these wraps a pipeline step whose command needs binaries from two conda packages. Galaxy's User-Defined Tools give a job exactly ONE container, so without a published multi-package image each step has to be split into two tools that pass files between them -- an extra workflow node, an extra staging round trip, and a second place for the logic to drift. The names are derivable (`mulled-hash`), and every one of these was checked against the Galaxy depot's 3,472 published `mulled-v2` images before being added here; none exists yet. gffread=0.12.7,python=3.12 gffread parses the GFF3, a Python helper reshapes it blast=2.17.0,python=3.12 dustmasker/windowmasker pipe into a Python interval classifier tantan=51,python=3.12 same shape, tantan instead of BLAST fastan=0.8,fastga=1.5.20260729 FasTAN scans, FastGA builds the GDB and reads the .1ano python=3.12,pyfaidx=0.9.0.4 random access to assemblies from a Python triage step multiz=11.2,python=3.12 multiz folds the MAFs, Python drives the fold order python=3.12,ucsc-bedtobigbed=469 a Python hub builder that shells out to bedToBigBed Every version pinned above already has a published single-package image, so each pair should resolve. `lastz=1.0.4,python=3.9` is the existing precedent for this shape. --- combinations/hash.tsv | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/combinations/hash.tsv b/combinations/hash.tsv index c89befa59..ba493c813 100644 --- a/combinations/hash.tsv +++ b/combinations/hash.tsv @@ -950,3 +950,10 @@ manc_cojo=1.1.0,tabix=1.11 lastz=1.0.4,python=3.9 aoptk=0.5.0,pyyaml=6.0.3 multiqc=1.35,oncoanalyser::oncoanalyser-multiqc-plugin=0.1.0 +gffread=0.12.7,python=3.12 +blast=2.17.0,python=3.12 +tantan=51,python=3.12 +fastan=0.8,fastga=1.5.20260729 +python=3.12,pyfaidx=0.9.0.4 +multiz=11.2,python=3.12 +python=3.12,ucsc-bedtobigbed=469