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External Tools And Runtime Notes

Some wrappers depend on external source trees or helper binaries outside the Python package itself.

Wrappers That Need External Tools

Model External tools needed
CalicoST CalicoST, Eagle_v2.4.1
Clonalscope_NoWGS clonalscope
Clonalscope_WGS clonalscope
Numbat numbat, Eagle_v2.4.1
Xclone Eagle_v2.4.1

Install Commands

From the repository root, run:

mkdir -p external_tools
cd external_tools

wget https://storage.googleapis.com/broad-alkesgroup-public/Eagle/downloads/Eagle_v2.4.1.tar.gz
tar -xzf Eagle_v2.4.1.tar.gz
rm Eagle_v2.4.1.tar.gz

git clone https://github.com/raphael-group/CalicoST.git CalicoST
git clone https://github.com/seasoncloud/Clonalscope.git clonalscope
git clone https://github.com/kharchenkolab/numbat.git numbat

Expected layout:

external_tools/
├── CalicoST/
├── Eagle_v2.4.1/
├── clonalscope/
└── numbat/

Default Config Mapping

If you keep the default public layout, you usually do not need to change the external tool paths. The public model templates use:

project_settings:
  exts: "${root_dir}/external_tools"

With that setting, the default paths resolve as follows:

CalicoST:
  calicost_dir: "${exts}/CalicoST"
  eagle_dir: "${exts}/Eagle_v2.4.1"

Clonalscope_NoWGS:
  aux_data_dir: "${exts}/clonalscope/data-raw"

Clonalscope_WGS:
  aux_data_dir: "${exts}/clonalscope/data-raw"

Numbat:
  pileup_script: "${exts}/numbat/inst/bin/pileup_and_phase.R"
  eagle_path: "${exts}/Eagle_v2.4.1/eagle"
  genetic_map: "${exts}/Eagle_v2.4.1/tables/genetic_map_hg38_withX.txt.gz"

Xclone:
  eagle_path: "${exts}/Eagle_v2.4.1/eagle"
  genetic_map: "${exts}/Eagle_v2.4.1/tables/genetic_map_hg38_withX.txt.gz"

If you install these tools somewhere else, update project_settings.exts or the corresponding model-specific paths in your models.yaml.

Runtime Notes

  • conda: easiest for local debugging and direct inspection
  • docker: easiest for reproducible containerized runs
  • apptainer: usually the best fit on HPC systems

UMI / Cell Tag Reminder

For allele-aware wrappers such as Numbat and Xclone, make sure UMItag and cellTAG match your BAM tagging convention.

Examples:

  • some STpipeline outputs use UMItag: B3 and cellTAG: B0
  • some Slide-seq WARP outputs use UMItag: UR and cellTAG: CB

See Model Run for the model-side configuration fields.