Update Dockerfile

Dockerfile

@@ -8,23 +8,63 @@
 #
 #CMD ["python", "SVision"]
 
-FROM continuumio/miniconda3
+#FROM continuumio/miniconda3
 
-WORKDIR .
+#WORKDIR .
+#
+#COPY . .
+#
+#RUN conda env create -f environment.yml
+#
+## Make RUN commands use the new environment:
+#SHELL ["conda", "run", "-n", "svisionenv", "/bin/bash", "-c"]
+#
+## Demonstrate the environment is activated:
+#RUN echo "Make sure tensorflow is installed:"
+#RUN python -c "import pyvcf"
+#
+#ENV PATH /opt/conda/envs/svisionenv/bin:$PATH
 
-COPY . .
+# The code to run when container is started:
+#COPY SVision .
+#ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "svisionenv", "python"]
 
-RUN conda env create -f environment.yml
+#WORKDIR .
+#COPY environment.yml .
+#
+#RUN conda env create -f environment.yml
+#
+#SHELL ["conda", "run", "-n", "svisionenv", "/bin/bash", "-c"]
+#
+#RUN conda init bash
+#RUN echo "conda activate svisionenv" > ~/.bashrc
+#
+#RUN pip install SVision
 
-# Make RUN commands use the new environment:
-SHELL ["conda", "run", "-n", "svisionenv", "/bin/bash", "-c"]
+#RUN conda init bash \
+#    && conda activate sivsionenv \
 
-# Demonstrate the environment is activated:
-RUN echo "Make sure tensorflow is installed:"
-RUN python -c "import tensorflow"
+## Install required packages to conda environment
+#RUN pip install numpy==1.16.4 \
+#    && pip install scipy==1.5.4 \
+#    && pip install opencv-python-headless \
+#    && pip install intervaltree \
+#    && pip install beautifulsoup4 \
+#    && pip install pysam \
+#    && pip install pyvcf \
+#    && pip install tensorflow==1.14.0 \
+#    && pip install SVision
+#CMD ["/opt/conda/envs/svisionenv/bin/SVision", "--help"]
 
-ENV PATH /opt/conda/envs/svisionenv/bin:$PATH
 
-# The code to run when container is started:
-#COPY SVision .
-ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "svisionenv", "python"]
+FROM ubuntu:18.04
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update && apt-get install --assume-yes apt-utils
+RUN apt-get update && apt-get install -y git python3>=3.6 python3-pip
+
+RUN cd /tmp \
+    && git clone https://github.com/xjtu-omics/SVision.git \
+    && cd SVision \
+    && pip3 install . \
+    && cp -r /usr/local/bin/SVision /usr/bin/
+

environment.yml

@@ -6,13 +6,13 @@ channels:
   - defaults
 dependencies:
   - python=3.6
-  - tensorflow=1.14.0
-  - pip=21.1.3
-  - pysam=0.16.0
+  - pip
   - pip:
     - numpy==1.16.4
     - scipy==1.5.4
-    - opencv-python-headless==4.5.4.58
-    - beautifulsoup4==4.9.3
-    - intervaltree==3.1.0
-    - pyvcf
+    - opencv-python-headless
+    - beautifulsoup4
+    - intervaltree
+    - pyvcf
+    - tensorflow==1.14.0
+    - pysam

setup.py

@@ -34,7 +34,9 @@
 
       zip_safe=False,
       python_requires='>=3.6',
-      # install_requires=['scipy', 'beautifulsoup4', 'numpy==1.16'],
+      install_requires=['scipy==1.5.4', 'numpy==1.16.4', 'tensorflow==1.14.0',
+                        'pysam', 'pyvcf', 'intervaltree', 'opencv-python-headless', 'beautifulsoup4'],
+
       scripts=['SVision'],
 
       )