Liatir

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Beta support and troubleshooting ​

Liatir Beta focuses on one coherent local laboratory path: inspect data, run a single-cell AI workflow, inspect and reuse its outputs, and run a saved Nextflow workflow either directly or inside a Liatir pipeline. Optional Local MCP can request exact saved pipeline revisions while Liatir remains in control of authorization, Jobs and Results.

Current limits ​

  • macOS packages are built for Apple silicon only; Intel Macs are not supported.
  • Windows Nextflow runs through WSL2 Linux x86_64. Native Windows Nextflow, WSL1 and WSL ARM64 are not supported.
  • The bundled Native Tools — samtools, bcftools, seqkit, fastp, bwa, minimap2 — also run through WSL2 on Windows, for the same reason: they have no Windows build. WSL2 must be installed; nothing has to be installed inside it. Files on a network location (\\server\share\…) cannot be reached from WSL2 and are refused with an explanation; copy them to a drive on the computer first.
  • SnpEff and SnpSift are installed together on demand rather than bundled. They are Java programs, so Java 21 or newer must still be installed on your machine.
  • Liatir does not yet install Nextflow/Java or configure HPC and cloud executors.
  • On Windows, GPU AI Models run their Linux CUDA Runtime Box through WSL2. The NVIDIA GPU must be visible inside WSL2; if it is not, run wsl --update and restart WSL2.
  • AI Model availability is target-specific. The model selector shows only compatible installed assets.
  • Liatir pipelines orchestrate tools but do not replace Nextflow scheduling, cache, resume or DSL semantics.
  • Liatir is research software. Outputs require scientific review and are not a medical diagnosis.

Common problems ​

macOS says the developer cannot be verified ​

Do not bypass the warning. The official app is signed and notarized by Apple, so this means the copy did not come from the Download page: delete it and download it again from there. If the warning persists, include the package filename and version in a support report.

Windows asks whether to run an unknown installer ​

Liatir for Windows comes only from the Microsoft Store and has no separate installer. Do not run a file claiming to be one: install Liatir from the Download page instead.

Update check is unavailable ​

Development builds do not have a release feed, and Microsoft Store copies are updated by the Store. In an official package, confirm that the machine can reach updates.liatir.com over HTTPS and try again. An offline app remains usable: the startup check stays silent when it cannot connect, and only the update check needs connectivity.

Liatir will not update or restart ​

Open Jobs. Finish or cancel every running Job, then retry. Liatir refuses to replace or restart the app while scientific work is active.

A file is missing ​

Liatir stores references to source files. If a file was moved, open Data, select the missing entry and use Relocate. Existing run history keeps its association with the updated reference.

An AI Model cannot be installed ​

Check the model's operating-system, architecture, accelerator, memory and disk requirements. Liatir will not substitute an incompatible Runtime Box. Keep the error and diagnostics; do not loosen version or signature checks.

Nextflow is not ready ​

Verify that both nextflow and java are installed on the supported execution host and available on PATH. On Windows, install them inside an x86_64 WSL2 distribution rather than as an unofficial native Windows wrapper.

A run was interrupted ​

Reopen Liatir and inspect Jobs and Results. Liatir reconciles interrupted runs instead of leaving them falsely running. Nextflow -resume is an explicit expert action and is allowed only with a compatible saved definition and source revision.

An MCP client cannot connect or start a pipeline ​

Open Settings → Local MCP and confirm the server is on. Copy the current Server URL and bearer token again: rotating the token invalidates the old one, and the local port can change when Liatir restarts. Save and explicitly allow the pipeline's current revision. Then bring Liatir to the foreground to approve the individual request. If a file input is rejected, allow that registered file under Source files from Data and pass its artifact ID rather than a path. If Result listing is unavailable, review the separate Allow Results permission. See Local MCP for the complete safety boundary.

Report a problem ​

Include the Liatir version, operating system and architecture, the affected Job or Result identity, what you expected, and the exported diagnostics. Do not send private datasets, credentials, signing keys, patient identifiers, or complete environment-variable dumps.