Update pip installation

Dockerfile

@@ -12,37 +12,36 @@ COPY /environment.yaml "${HOME}/environment.yaml"
 COPY --chown=1000:100 main "${HOME}"/main
 
 # Install cobamp, bioservices, and troppo manually, as problems arose when installing using pip
-RUN git clone https://github.com/babessell1/cobamp.git \
-    && git clone https://github.com/babessell1/troppo.git \
-    && pip install ./cobamp \
-    && echo "COBAMP DONE" \
-    && pip install ./troppo \
-    && echo "TROPPO DONE" \
-    && rm -rf cobamp troppo \
-    && pip cache purge
+RUN git clone https://github.com/babessell1/cobamp.git && \
+    git clone https://github.com/babessell1/troppo.git && \
+    pip install ./cobamp ./troppo && \
+    rm -rf cobamp troppo && \
+    pip cache purge
 
 # Install python-related items
 # R channel will be placed at the bottom
-RUN conda config --quiet --add channels r \
-    && conda config --quiet --add channels bioconda \
-    && conda config --quiet --add channels conda-forge \
-    && mamba env update --name=base --file="${HOME}/environment.yaml" \
-    && R -e "devtools::install_github('babessell1/zFPKM')" \
+RUN conda config --quiet --add channels r && \
+    conda config --quiet --add channels bioconda && \
+    conda config --quiet --add channels conda-forge && \
+    mamba env update --name=base --file="${HOME}/environment.yaml" && \
+    pip install --quiet --upgrade pip && \
+    pip install "memote==0.13.0" "framed==0.5.2" "bioservices==1.11.2" "jupyterlab-spreadsheet-editor==0.6.1" && \
+    R -e "devtools::install_github('babessell1/zFPKM')" && \
     # Install gurbori
-    && wget --quiet --directory-prefix="${HOME}" https://packages.gurobi.com/${GRB_SHORT_VERSION}/gurobi${GRB_VERSION}_linux64.tar.gz \
-    && tar -xf "${HOME}/gurobi${GRB_VERSION}_linux64.tar.gz" \
-    && rm -f "${HOME}/gurobi${GRB_VERSION}_linux64.tar.gz" \
-    && mv ${HOME}/gurobi* ${HOME}/gurobi \
-    && rm -f "${HOME}/environment.yaml" \
-    && rm -r "${HOME}/work" \
-    && pip cache purge \
-    && conda clean --all --yes --force-pkgs-dirs
+    wget --quiet --directory-prefix="${HOME}" https://packages.gurobi.com/${GRB_SHORT_VERSION}/gurobi${GRB_VERSION}_linux64.tar.gz && \
+    tar -xf "${HOME}/gurobi${GRB_VERSION}_linux64.tar.gz" && \
+    rm -f "${HOME}/gurobi${GRB_VERSION}_linux64.tar.gz" && \
+    mv ${HOME}/gurobi* ${HOME}/gurobi && \
+    rm -f "${HOME}/environment.yaml" && \
+    rm -r "${HOME}/work" && \
+    pip cache purge && \
+    conda clean --all --yes --force-pkgs-dirs
 
 # Update jupyter notebook configuration
-RUN jupyter trust "${HOME}/main/COMO.ipynb" \
-    && echo "c.ServerApp.ip = '0.0.0.0'" >> "${HOME}/.jupyter/jupyter_notebook_config.py" \
-    && echo "c.ServerApp.root_dir = '${HOME}/main'" >> "${HOME}/.jupyter/jupyter_notebook_config.py" \
-    && echo "c.ServerApp.token = ''" >> "${HOME}/.jupyter/jupyter_notebook_config.py" \
-    && echo "c.ServerApp.password = ''" >> "${HOME}/.jupyter/jupyter_notebook_config.py"
+RUN jupyter trust "${HOME}/main/COMO.ipynb" && \
+    echo "c.ServerApp.ip = '0.0.0.0'" >> "${HOME}/.jupyter/jupyter_notebook_config.py" && \
+    echo "c.ServerApp.root_dir = '${HOME}/main'" >> "${HOME}/.jupyter/jupyter_notebook_config.py" && \
+    echo "c.ServerApp.token = ''" >> "${HOME}/.jupyter/jupyter_notebook_config.py" && \
+    echo "c.ServerApp.password = ''" >> "${HOME}/.jupyter/jupyter_notebook_config.py"
 
 VOLUME /home/joyvan/main/data/local_files

environment.yaml

@@ -54,10 +54,9 @@ dependencies:
   - python-libsbml==5.19.2
   - optlang==1.5.2
   - cobra==0.25.0
-  - pip==22.1.2
-  - pip:
-    - memote==0.13.0
-    - framed==0.5.2
-    - bioservices==1.11.2
-    - jupyterlab-spreadsheet-editor==0.6.1
-
+#   - pip==22.1.2
+#   - pip:
+#     - memote==0.13.0
+#     - framed==0.5.2
+#     - bioservices==1.11.2
+#     - jupyterlab-spreadsheet-editor==0.6.1