Supporting Information
Supporting information for Galaxy Notebooks: Reproducible Communication for Data-Intensive Analysis. Every item is a real, committed artifact from the three worked vignettes; together they let a reader re-run each analysis and re-extract its workflow.
The bundle lives in si/ beside the manuscript. Recipes render as pages (linked below); workflow .ga files and tool-install YAMLs are downloadable from the deployed site under /galaxy-brain/si/ and are also in si/ for local use.
Caveats (read before relying on these). Tool versions and parameters are pinned to the reference development server (Galaxy 26.2.dev0). Encoded dataset/collection identifiers are instance-specific; the recipes give the step to regenerate them rather than hard-coding them. Before journal submission these should be re-confirmed against the merged release and trimmed to the target’s SI length limit.
Numbering note. SI item numbers preserve the original internal use-case order. In the manuscript, differential ATAC-seq is Vignette 2 but remains Recipe S3 / Workflow S5 here; differential ChIP is Vignette 3 but remains Recipe S2 / Workflows S2-S4.
Contents
| SI item | What it is | Vignette | File | Source |
|---|---|---|---|---|
| Recipe S1 | Server-agnostic reproduction recipe | Vignette 1: mobile resistome (internal UC1) | SI_Recipe_S1_mobile_resistome | usecases/UC1_RECIPE.md |
| Recipe S2 | Server-agnostic reproduction recipe | Vignette 3: differential ChIP (internal UC2) | SI_Recipe_S2_differential_chip | usecases/UC2_RECIPE.md |
| Recipe S3 | Server-agnostic reproduction recipe | Vignette 2: differential ATAC-seq (internal UC3) | SI_Recipe_S3_differential_atac | usecases/UC3_RECIPE.md |
| Workflow S1 | Extracted 14-step workflow | Vignette 1: mobile resistome (internal UC1) | SI_Workflow_S1 | UC1_MRSA_extracted.ga |
| Workflow S2 | Single extraction, condition-pinned (34-step) | Vignette 3: differential ChIP (internal UC2) | SI_Workflow_S2 | UC2_TAL1_single_condition-pinned.ga |
| Workflow S3 | Map-over peak caller (5-step) | Vignette 3: differential ChIP (internal UC2) | SI_Workflow_S3 | UC2_TAL1_peak_caller.ga |
| Workflow S4 | Pairwise comparator (29-step) | Vignette 3: differential ChIP (internal UC2) | SI_Workflow_S4 | UC2_TAL1_comparator.ga |
| Workflow S5 | Extracted 13-step workflow | Vignette 2: differential ATAC-seq (internal UC3) | SI_Workflow_S5 | usecases/UC3_ATAC_extracted_figures.ga |
| Data S1 | ephemeris/shed-tools install list | Vignette 1: mobile resistome (internal UC1) | SI_Data_S1 | mrsa-mobile-amr-tools.yml |
| Data S2 | ephemeris/shed-tools install list | Vignette 3: differential ChIP (internal UC2) | SI_Data_S2 | tal1-candidate-genes-tools.yml |
| Data S3 | ephemeris/shed-tools install list | Vignette 2: differential ATAC-seq (internal UC3) | SI_Data_S3 | atac-differential-tools.yml |
Reproduction recipes
- SI_Recipe_S1_mobile_resistome — four-isolate S. aureus ARG↔IS proximity analysis (BioProject PRJDB8599). Notable: the
remove_short_is=truegotcha that governs byte-identical reproduction. - SI_Recipe_S3_differential_atac — differential ATAC-seq accessibility (DESeq2 → NA-filter → volcano / ranked top-gained tables); figures kept on-graph by converting each PDF to PNG with an in-graph tool so extraction seeds the full 13-step pipeline.
- SI_Recipe_S2_differential_chip — TAL1 differential binding between two blood-cell lineages (mm10, MACS2); documents the nested
list:listdesign encoding and the caller/comparator split.
Extracted workflows
Import any .ga directly into Galaxy (Workflows → Import). Workflows S1 and S5 are the clean baselines; S2 is the runnable-but-condition-pinned single ChIP extraction; S3 + S4 are the reusable decomposition of S2 (map-over caller + pairwise comparator).
Tool-install lists
Install per vignette with shed-tools install -g <server> -a <key> -t <SI_Data_*.yml> --skip-install-resolver-dependencies (ephemeris installed isolated via uv tool). Each recipe also lists confirmed tool IDs and versions inline.
Not included
The UC*_DEBRIEF*.md and UC*_PAPER_INTEGRATION.md files under usecases/ are internal working notes, not supporting information.