added docker container

Dockerfile

@@ -0,0 +1,6 @@
+FROM quay.io/comp-bio-aging/base:latest
+
+WORKDIR /opt/yspecies
+ADD ./ /opt/yspecies
+RUN micromamba env create -y -f /opt/yspecies/environment.yaml
+ENV ENV_NAME="yspecies"

README.md

@@ -62,6 +62,10 @@ Getting started
 -------------------
 First you have to create a [Conda environment](https://docs.conda.io/en/latest/miniconda.html) or [Micromamba environment](https://github.com/mamba-org/mamba) for the project:
 Micromamba is a superior alternative to Conda with very similar API.
+Alternatively, you can use docker container that already contains micromamba environment with everything pre-installed:
+```
+docker run -i -t quay.io/comp-bio-aging/yspecies:latest
+```
 
 To create environment you can do:
 ```bash

build-docker.sh

@@ -0,0 +1,2 @@
+#!/usr/bin/env bash
+docker build -t quay.io/comp-bio-aging/yspecies:latest .

environment.yaml

@@ -5,20 +5,21 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python=3.8
-  - jupyterlab=3.0.14
-  - dvc=2.0.18
+  - python=3.9
+  - jupyterlab=3.2.3
+  - dvc=2.8.3
+  - dvc-gdrive=2.8.3
   - papermill=2.3.3
-  - anaconda-client=1.7.2
-  - conda-build=3.21.4
-  - mamba=0.10.0
-  - scikit-learn=0.24.1
-  - seaborn=0.11.1
-  - more-itertools=8.7.0
-  - lightgbm=3.2.0
-  - statsmodels=0.12.2
-  - click=7.1.2
+  - scikit-learn=1.0.1
+  - anaconda-client=1.9.0
+  - conda-build=3.21.6
+  - mamba=0.17.0
+  - scikit-learn=1.0.1
+  - more-itertools=8.11.0
+  - lightgbm=3.2.1
+  - statsmodels=0.13.1
+  - click=8.0.3
   - loguru=0.5.3
-  - plotly=4.14.3
-  - shap=0.37.0
-  - optuna=2.7.0
+  - plotly=5.3.1
+  - shap=0.40.0
+  - optuna=2.10.0

notebooks/select_samples.ipynb

@@ -6756,7 +6756,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -6770,7 +6770,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,