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rjbohlender merged 1 commit into from
Sep 29, 2025
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Update README.md #28

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21 changes: 15 additions & 6 deletions README.md
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Expand Up @@ -111,24 +111,29 @@ cmake -DCMAKE_BUILD_TYPE=Release -DLAPACK_LIBRARIES=/usr/lib/x86_64-linux-gnu/op

---

The "reduce" step of IBDMap is done by the `ibdreduce.py` script. This script is built for Python >=3.9 and <4.0.
The "reduce" step of IBDMap is done by the `ibdreduce.py` script. This script is built for Python >=3.9.

IBDReduce requires the following Python packages:

* `numpy` (>=1.26.4 and <2.0.0)
* `scipy` (>=1.13.0 and <2.0.0)
* `zstandard` (>=0.22.0 and <1.0.0)

These dependencies are listed in the `pyproject.toml` file within the IBDReduce subdirectory. You can use`pip` to install dependencies directly from this file with the following command:
These dependencies are listed in a requirements.txt file with the IBDReduce sub directory. It is recommend that you install the dependencies into a virtualenv such as conda or venv. The requirements.txt file was made from a python3.11 environment to be consistent with the docker environment so it is recommend that you use python3.11

```bash
cd ./IBDReduce && pip install .
# virtual environment creation (python3.11 must be install)
python3.11 -m venv venv
# activate environment
source venv/bin/activate
# use pip to install required packages
pip install --upgrade pip && pip install -r IBDReduce/requirements.txt
```
Before running IBDReduce, make sure that this environment is activate otherwise you will get an error saying the dependencies are not installed.

*note on virtual environments:*
We recommend installing dependencies and running IBDReduce inside a [venv](https://docs.python.org/3/library/venv.html) or [conda](https://docs.conda.io/projects/conda/en/stable/user-guide/tasks/manage-environments.html) environment. All Python dependencies are also installed automatically if using the Docker build steps.



## Execution

### IBDMap
Expand Down Expand Up @@ -165,7 +170,7 @@ IBDReduce requires several inputs:

---

We have provided a Dockerfile in the top level IBDMap folder for streamlined building and execution. The same Docker image is additionally available at Dockerhub here: https://hub.docker.com/r/jtb114/ibdmap
We have provided a Dockerfile in the top level IBDMap folder for streamlined building and execution. The same Docker image is additionally available at Dockerhub here: https://hub.docker.com/r/jtb114/ibdmap. This image includes both the ibdmap executable and the ibdreduce script

#### Pulling from Dockerhub

Expand All @@ -184,11 +189,15 @@ This command will create a new singularity image called `ibdmap.sif`. The tool c
```bash
# Docker image
docker run --rm {image ID/tag} ibdmap -h
docker run --rm {image ID/tag} python3 /app/ibdreduce_v3.py -h

# Singularity image
singularity exec ibdmap.sif ibdmap -h
singularity exec ibdmap.sif python3 /app/ibdreduce_v3.py -h
```

*note:* the ibdreduce script is kept in the /app/ folder of the image so it is required to specify the full path as shown above otherwise you will get an error

## Data Formatting

### Inputs
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