add scpy

scpy/Dockerfile

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+FROM mambaorg/micromamba:2-ubuntu22.04 AS source
+
+USER $MAMBA_USER
+
+# set work directory
+WORKDIR /tmp
+
+# copy environment file
+COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
+
+# create environment from yml file
+RUN micromamba env create -f environment.yml \
+  && micromamba clean --all --yes \
+  && rm /tmp/environment.yml
+
+FROM mambaorg/micromamba:2-ubuntu22.04 AS final
+
+ARG BUILD_VERSION=v0.1
+
+################## METADATA ######################
+LABEL base_image="micromamba:2-ubuntu22.04"
+LABEL version="1"
+LABEL software="scpy utilities"
+LABEL software.version="${BUILD_VERSION}"
+LABEL about.summary="Python data science utilities for single-cell omics data"
+LABEL about.tags="Genomics"
+LABEL about.license="MIT"
+
+COPY --from=source /opt/conda/envs/scpy /opt/conda/envs/scpy
+
+# Won't be activated unless you we login via /bin/bash command
+# RUN echo "micromamba activate fastcat" >> ~/.bashrc 
+
+# set fastcat as the default environment
+# !!! this step is important or you cannot packages installed in this environment
+ENV ENV_NAME scpy
+ENV PATH=/opt/conda/envs/scpy/bin:$PATH
+
+WORKDIR /app
+
+# default command
+CMD ["python", "--help"]
+
+# add mantainer
+MAINTAINER Haidong Yi <[email protected]>

scpy/README.md

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+# Scpy Docker Image
+
+This Dockerfile builds a docker image (`scpy`) for python's data science utilities in single-cell data analysis. In this image, we bundled a few python packages:
+
+- numpy
+- pandas
+- scipy
+- polars
+- editdistance
+- umi_tools
+
+These python packages are useful in many applications of single-cell omics data analysis, especially for processing mapping and tagging results.
+
+## Build
+
+To build the image:
+
+```bash
+docker build -t scpy:v0.1 .
+```
+
+You can specify a different version using the `BUILD_VERSION` argument:
+
+```bash
+docker build --build-arg BUILD_VERSION={your_version} -t scpy:{your_version} .
+```
+
+## Usage
+
+Run the container:
+
+```bash
+docker run --rm scpy:v0.1 python --help
+```
+
+This will display the help message for `Python`. To run specific commands, replace `python --help` with your desired commands that run python scripts.
+
+## Features
+
+- Created based on `micromamba` image
+- Bundled with useful python packages (e.g. `numpy`, `panads` and `polars` etc.)
+- For single-cell data analysis, we also added the python packages: `editdistance` and `umi_tools`.
+
+## License
+
+This docker image is released under the MIT License.

scpy/environment.yml

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+name: scpy
+channels:
+    - conda-forge
+    - bioconda
+    - defaults
+dependencies:
+    - python ==3.8.19
+    - h5py ==3.11.0
+    - numpy ==1.23.5
+    - scipy ==1.10.1
+    - pandas ==2.0.3
+    - polars ==0.20.22
+    - editdistance ==0.6.2
+    - gcc
+    - pip
+    - pip:
+      - umi_tools ==1.1.2

scpy/version

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+v0.1