Non-containerized

Non-containerized installation

CBIcall and its external bioinformatics resource bundle are installed separately. The Python package contains the driver, workflow definitions, schemas, catalogs, report assets, and integration-test fixtures. Reference genomes and third-party bioinformatics tools remain in the external bundle.

Install CBIcall

Method 1: PyPI (recommended)

Install the core command:

python3 -m pip install --upgrade cbicall
cbicall --version

Install the optional Snakemake and MultiQC Python dependencies when needed:

python3 -m pip install --upgrade "cbicall[all]"

Nextflow and Cromwell are external executables and are not installed as Python dependencies. Bash workflows need neither engine.

Method 2: Source checkout (development)

Use an editable install for development:

git clone https://github.com/CNAG-Biomedical-Informatics/cbicall.git
cd cbicall
python3 -m pip install -e ".[all,test]"
pytest

After either installation method, use cbicall directly. The repository launcher bin/cbicall remains available for source-checkout compatibility.

Choose a workflow path

Workflow path	CBIcall bundle required?	Additional runtime
External nf-core provider	No	Nextflow and the selected nf-core profile, such as Docker or Apptainer.
Native Bash, Snakemake, Nextflow, or Cromwell WES/WGS	Yes	The selected workflow backend and the CBIcall resource bundle.
Native Bash mtDNA	Yes	x86_64 host and the CBIcall resource bundle.

The nf-core demo can be validated and launched without the native bundle:

cbicall validate-parameters -p examples/input/nf-core-demo.yaml --no-color
cbicall run -p examples/input/nf-core-demo.yaml -t 4 --no-color

Install resources for native workflows

Choose a persistent directory for the external bundle:

export CBICALL_DATA=/absolute/path/to/cbicall-data
mkdir -p "$CBICALL_DATA"
cbicall install-resources --outdir "$CBICALL_DATA"

To verify only the small catalog-pinned resource identifier before downloading the large archive:

cbicall install-resources \
  --outdir "$CBICALL_DATA" \
  --verify-resource-id-only

Google Drive may restrict large automated downloads. Print the manual download list when necessary:

cbicall install-resources \
  --outdir "$CBICALL_DATA" \
  --print-manual-download

Place every listed file in $CBICALL_DATA, then resume assembly, checksum verification, extraction, and manifest creation:

cbicall install-resources \
  --outdir "$CBICALL_DATA" \
  --skip-download

The installer:

• downloads missing split files when possible;
• reassembles the archive;
• verifies the catalog-declared checksums;
• validates the optional SHA-256-pinned resource identifier;
• extracts Databases/ and NGSutils/;
• writes cbicall-resource-installation.json with installation provenance.

Add --remove-parts after successful verification when disk space is limited.

Configure the resource location

Set CBICALL_DATA in every shell or scheduler environment used to launch native workflows:

export CBICALL_DATA=/absolute/path/to/cbicall-data
cbicall doctor
cbicall validate-parameters -p examples/input/param.yaml

The same variable is passed consistently to native Bash, Snakemake, Nextflow, and Cromwell workflows and is recorded in the execution contract. Checked-in backend paths remain fallbacks for existing source and institutional profiles.

Run integration tests

cbicall test --wes-bash -t 1
cbicall test --mit-bash -t 1

Source-checkout tests write under examples/input. Installed-package tests stage the packaged fixtures in a temporary directory and print that directory so generated reports can be inspected.

System requirements

• Linux on amd64 or arm64; macOS can be used with a Linux VM.
• Python 3.8 or newer.
• Java 17 for current GATK 4.6 workflows.
• libncurses.so.5 and libtinfo.so.5 compatibility libraries for bundled legacy tools.
• At least 16 GB RAM and 100 GB disk for the native resource bundle and test workflows.

The mtDNA workflow uses MToolBox and is supported on x86_64 only.