dockerfile from codeocean

README.md

@@ -52,6 +52,9 @@ provided in the ```install/requirements.txt``` file; for example:
 
 To deactivate the environment: ```$> deactivate```
 
+Alternatively, Cue can be installed using the```Dockerfile``` provided in the ```install/docker``` directory 
+from Cue's capsule in CodeOcean.
+
 <a name="demo"></a>
 ### Tutorial
 

install/docker/Dockerfile

@@ -0,0 +1,48 @@
+FROM registry.codeocean.com/codeocean/miniconda3:4.7.10-python3.7-ubuntu18.04
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+        bcftools=1.7-2 \
+        build-essential=12.4ubuntu1 \
+        libbz2-dev=1.0.6-8.1ubuntu0.2 \
+        zlib1g-dev=1:1.2.11.dfsg-0ubuntu2.1 \
+        libgl1-mesa-glx \
+        libglib2.0-0 \
+        libsm6 \
+        libxrender1 \
+        libxext6 \
+        tabix \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN pip install --upgrade pip
+
+RUN pip install -U --no-cache-dir \
+    setuptools==58.0.0 \
+    wheel
+RUN pip install -U --no-cache-dir \
+    bitarray==1.6.3 \
+    cachetools==4.1.0 \
+    cython==0.29.21 \
+    intervaltree==3.1.0 \
+    joblib==0.16.0 \
+    matplotlib==3.2.1 \
+    numpy==1.18.5 \
+    opencv-python==4.5.1.48 \
+    pandas==1.0.5 \
+    pycocotools==2.0.4 \
+    pyfaidx==0.5.9.5 \
+    pysam==0.16.0.1 \
+    pytabix==0.1 \
+    python-dateutil==2.8.1 \
+    pyyaml==5.3.1 \
+    seaborn==0.11.0 \
+    setuptools-scm==6.4.2 \
+    torch==1.5.1 \
+    torchvision==0.6.1 \
+    jupyter
+
+RUN python3 -m pip install Truvari
+
+ENV PYTHONPATH "${PYTHONPATH}:/code"