Installing ChoCallate

ChoCallate is tested on Linux. macOS and Windows are not currently tested.

Requirements

• Conda (Miniconda/Anaconda) or Mamba
• Git

Installation on Linux using conda

To install the latest ChoCallate version, follow these steps.

Clone the repository

git clone --depth 1 https://github.com/alermol/ChoCallate.git

Create and activate the environment

cd ChoCallate
conda env create -y -f environment.yaml
conda activate ChoCallate

Verify the installation (optional)

cd test_run
bash run_test.sh

Clean up test output (optional)

bash cleanup.sh

Use the Docker container

1. Install Docker using the official instructions.

2. Pull the latest image from DockerHub

docker pull alermol/chocallate:latest

3. Prepare a working directory with your input files

input_data
├── reads
|   ├── sample1_F.fq
|   ├── sample1_R.fq
|   ├── sample2_F.fq
|   └── sample2_R.fq
├── samples.tsv
├── config.yaml
├── include.bed
├── exclude.bed
├── genome_assembly.fna
└── genome_assembly.fna.mmi

The folder structure can be different. Just make sure the file paths in config.yaml and samples.tsv match the paths inside the container (in the container default $WORKDIR is /workspace).

Example config.yaml paths (mounted root is /workspace):

input:
  samples_tsv: /workspace/samples.tsv
  reference_genome: /workspace/genome_assembly.fna
  reference_index_dir: /workspace/
  include_bed: /workspace/include.bed
  exclude_bed: /workspace/exclude.bed
...
output:
  directory: /workspace/ChoCallate_output

Example samples.tsv (TAB-separated):

sample1<TAB>/workspace/reads/sample1_F.fq<TAB>/workspace/reads/sample1_R.fq
sample2<TAB>/workspace/reads/sample2_F.fq<TAB>/workspace/reads/sample2_R.fq

4. Run ChoCallate

docker run --rm \
  -u "$(id -u):$(id -g)" \
  -v "${PWD}/input_data:/workspace" \
  -w /workspace \
  alermol/chocallate:latest \
  -params-file config.yaml

Wait for completion.

5. Output results will appear in ChoCallate_output inside your input_data directory

input_data
├── reads
|   ├── sample1_F.fq
|   ├── sample1_R.fq
|   ├── sample2_F.fq
|   └── sample2_R.fq
├── ChoCallate_output
|   ├── consensus.bcf
|   ├── pipeline_report.html
|   ├── timeline_report.html
|   └── trace.txt
├── samples.tsv
├── config.yaml
├── include.bed
├── exclude.bed
├── genome_assembly.fna
└── genome_assembly.fna.mmi