Add seven two-package combinations for the BRC pangenome tool set - #4131
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richard-burhans wants to merge 1 commit into
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Add seven two-package combinations for the BRC pangenome tool set#4131richard-burhans wants to merge 1 commit into
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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.
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Seven two-package combinations, all for steps in the BRC pangenome tool set.
Each wraps a command that needs binaries from two conda packages. Galaxy's User-Defined Tools give a job exactly one container, so with no published multi-package image each of these steps 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.
gffread=0.12.7,python=3.12blast=2.17.0,python=3.12tantan=51,python=3.12fastan=0.8,fastga=1.5.20260729.1anopython=3.12,pyfaidx=0.9.0.4multiz=11.2,python=3.12python=3.12,ucsc-bedtobigbed=469bedToBigBedChecked before opening:
mulled-hashand looked up against the depot's 3,472 publishedmulled-v2images;lastz=1.0.4,python=3.9is already inhash.tsv, so this is the established shape rather than a new one.Happy to split this into separate PRs if one combination is contentious.