Working in the app

Resource Center.

Some nodes need something that is not your data: a probe manifest, a ligand-receptor database, a pretrained model, a prior network, a genome. 14 such resources feed 15 nodes. The Resource Center is where they are installed once, verified, licence-accepted, and shared by every workflow on the machine.

The rule: a run never downloads

Before a node executes, Oreumics resolves the exact version it will use, checks its SHA-256, and takes a lease on it. Only then does it load your data. Nothing is fetched in the middle of a run, so a long analysis cannot silently change its own inputs, stall on someone else’s server, or produce results you cannot reproduce later because “the database moved on”. The version and digest are written into the result’s provenance.

What this changes for you: a template containing one of these nodes will not run end to end on a fresh install. Every other node runs normally and the gated one stops with a message naming the missing resource (v0.25.0 — previously a lease error). That is the intended behaviour, not a failure: set the resource up once and the template runs clean from then on.

Opening it

Click the resource status chip in the toolbar. It changes colour when something a workflow on your canvas needs is not ready.
Or use the Setup card at the top of a gated node’s Properties panel, which opens the Resource Center focused on exactly the resource that node is waiting for.
The AI Copilot and connected assistants can ask which resources are installed (get_resource_status) before proposing a plan, so a plan does not send you into a node that will stop.

What ships, what downloads, what you supply

Resource	Used by	Comes from
Illumina Methylation Manifest Probe coordinates and Type I / II design for 27K, 450K, EPIC v1, EPIC v2 and Mouse arrays, supplied by methylprep or mepylome. Recognised from the methylprep / mepylome manifest cache on your machine, or a file you choose. `methyl.manifest`	Load IDAT Load Methyl Beta Matrix	Cache or your file
Extended Methylation Probe Annotation Zhou-lab / UCSC gene and positional annotation used to name the genes behind a DMP or DMR and to feed GOmeth. Cached per array under the Oreumics profile folder. `methyl.annotation`	Load IDAT Load Methyl Beta Matrix Methyl GOmeth	Cache or your file
ENCODE SCREEN cCRE Candidate cis-regulatory elements (hg38 BED) for testing whether your DMPs fall in promoters or enhancers. `encode.ccre`	DMP Feature Enrichment	Your file
JASPAR Motif Database JASPAR CORE position-frequency matrices for motif scanning. JASPAR2020 / 2022 / 2024 / 2026 all ship inside the installer; the default is JASPAR2022. `jaspar.motifs`	Motif Analysis	Bundled
Reference Genome FASTA Your own genome assembly (hg38, mm10 …), needed to read the sequence under a peak. Referenced in place, not copied. `genome.fasta`	Motif Analysis	Your file
CellPhoneDB Database A versioned CellPhoneDB database archive. The app bundles the CellPhoneDB code, not its database. An existing ~/.cpdb release is recognised; otherwise choose the zip you obtained from CellPhoneDB. `cellphonedb.database`	CellPhoneDB	Cache or your file
OmniPath Intercell Network A pinned intercellular network snapshot for squidpy ligand-receptor testing. Licence purpose (academic / commercial / non-profit) must be chosen and accepted. `omnipath.intercell`	Ligand-Receptor	Download
LIANA Ligand-Receptor Bundle Consensus, mouse consensus, CellChatDB, CellPhoneDB and connectomeDB resources shipped with the pinned LIANA package. `liana.lr`	LIANA Spatial Ligand-Receptor	Bundled
CellTypist Model A pretrained CellTypist model for per-cell annotation (Immune_All_Low by default). An existing ~/.celltypist model cache is recognised; otherwise choose the .pkl you downloaded. `celltypist.model`	CellTypist Annotation	Cache or your file
PROGENy Prior Network Signed pathway-responsive gene weights for pathway activity inference (human). Licence purpose must be chosen and accepted. `progeny.prior`	PROGENy Activity	Download
MSigDB Hallmark Gene Sets The fifty Hallmark gene sets, scored as continuous activity (human). MSigDB terms must be accepted. `msigdb.hallmark`	Hallmark Activity	Download
CollecTRI Regulon Curated signed TF-target interactions for transcription-factor activity inference (human), pinned to a Zenodo record. `collectri.regulon`	CollecTRI TF Activity	Download
Gene-set Library A managed or user-supplied GMT / table for over-representation analysis, human or mouse — the local alternative to Enrichr. `geneset.library`	Pathway Enrichment GSEA / ORA Methyl GOmeth	Your file
Enrichr Remote Analysis The online Enrichr service. The only resource that is queried rather than installed — see “What leaves your machine”. `enrichr.service`	Pathway Enrichment GSEA / ORA Methyl GOmeth	Remote service

Bundled ships inside the installer and works offline. Download is fetched once from the source shown in the dialog, after you accept its terms. Your file cannot be fetched for you — licensing or sheer size means you point Oreumics at a copy you already have. Cache or your file means Oreumics first looks in the tool’s own cache on your machine and otherwise asks for the file.

What the statuses mean

Ready: Installed, verified, and usable right now. Nothing to do.
Setup required: Nothing is configured for this resource yet. Open it and pick a version, a variant or a file.
Download required: A version is selected but not yet fetched. Press Install — this is the moment Oreumics goes to the network, never during a run.
License review required: The source imposes terms you have not accepted yet. Review terms shows them with the link, and waits.
Local file required: This one cannot be downloaded for you — Choose file points it at a copy you already have (a genome FASTA, a cCRE BED, a gene-set table, a CellPhoneDB zip).
Verification failed: What is on disk no longer matches the recorded checksum. Repair re-installs the same version; it never silently substitutes a different one.
Online access required: A remote service is needed and the app is currently not allowed to reach it.
Not configured / Unavailable / Incompatible / Species mismatch: Less common states: no selection was made, the provider cannot serve this variant, or the chosen file does not match the data’s organism.

The buttons follow the status: Install, Review terms (then Accept and install), Choose file, Repair, and Refresh to re-check the store.

What leaves your machine

Installing a resource sends only a selector — which version, which organism, which model — and downloads the file. Your matrices, cells and coordinates are never part of that exchange.

One exception: Enrichr

Pathway Enrichment, GSEA and Methyl GOmeth can call the online Enrichr service, which works by receiving your gene symbols and returning enriched terms. No expression values, no per-cell data, no sample metadata — but the gene list itself does travel. If that is not acceptable for your data, supply a local gene-set library instead and the analysis stays entirely on the machine.

Storage

Installed resources live in one managed store, addressed by content, and shared across every project — a prior downloaded for one workflow is reused by the next. The dialog shows Managed resource storage with how much of the quota is in use. Downloaded resources are marked evictable when space runs low and can be re-installed at the same version; bundled data is not stored there at all; files you supplied yourself are referenced in place and never deleted for you.

Recent changes

v0.25.0 — a node whose resource is missing stops with a message naming the resource instead of a lease error.
v0.25.0 — CellPhoneDB databases installed through the Resource Center are recognised by the CellPhoneDB node.
v0.25.0 — the AI can ask which resources are installed (get_resource_status) before proposing a plan.
v0.25.0 — Motif Analysis fails loudly when its motif database is missing rather than quietly returning nothing.
v0.22.1 — the installed app ships the JASPAR releases the Resource Center lists; JASPAR2026 is selectable.
v0.22.0 — the Resource Center itself: CellPhoneDB, CellTypist and OmniPath stopped downloading inside a run.

Methylation tutorial — needs a probe manifest and, for GOmeth, the extended annotation.
Visium tutorial — the Ligand-Receptor step needs the OmniPath intercell network.
ATAC tutorial — JASPAR is bundled; scanning sequence also wants a genome FASTA.
Templates — which shipped templates stop at a gated node.