changed based image template to avoid cfg issues

wc_env_manager/assets/base_image/Dockerfile.template

@@ -101,20 +101,33 @@ RUN apt-get update -y \
     && apt-get autoremove -y \
     && rm -rf /var/lib/apt/lists/*
 
+# Java
+{% if java_install -%}
+RUN apt-get update -y \
+    && apt-get install -y --no-install-recommends \
+        default-jre \
+    && rm -rf /var/lib/apt/lists/*
+{%- endif %}
+
 # Node
+{% if npm_install -%}
 RUN apt-get update -y \
     && apt-get install -y --no-install-recommends \
         nodejs \
         npm \
     && rm -rf /var/lib/apt/lists/
+{%- endif %}
 
 # curl
+{% if curl_install -%}
 RUN apt-get update -y \
     && apt-get install -y --no-install-recommends \
         curl \
     && rm -rf /var/lib/apt/lists/
+{%- endif %}
 
 # install PostgreSQL client
+{% if postgresql_client_install -%}
 RUN apt-get update -y \
     && apt-get install -y --no-install-recommends \
         gnupg \
@@ -131,8 +144,10 @@ RUN apt-get update -y \
         wget \
     && apt-get autoremove -y \
     && rm -rf /var/lib/apt/lists/*
+{%- endif %}
 
 # install openbabel
+{% if openbabel_install -%}
 ARG openbabel_version=2.4.1
 RUN apt-get update -y \
     && apt-get install -y --no-install-recommends \
@@ -171,8 +186,11 @@ RUN apt-get update -y \
         zlib1g-dev \
     && apt-get autoremove -y \
     && rm -rf /var/lib/apt/lists/*
+{%- endif %}
 
 # install ChemAxon Marvin
+
+{% if marvin_install -%}
 ARG marvin_version=19.7
 COPY marvin_linux_${marvin_version}.deb /tmp/
 RUN apt-get update -y \
@@ -187,23 +205,9 @@ RUN apt-get update -y \
     && rm -rf /var/lib/apt/lists/*
 ENV JAVA_HOME=/usr/lib/jvm/default-java \
     CLASSPATH=$CLASSPATH:/opt/chemaxon/marvinsuite/lib/MarvinBeans.jar
+{%- endif %}
+
 
-# Docker
-RUN apt-get update -y \
-    && apt-get install -y --no-install-recommends \
-        apt-transport-https \
-        ca-certificates \
-        curl \
-        software-properties-common \
-    && curl -fsSL https://download.docker.com/linux/ubuntu/gpg | apt-key add - \
-    && add-apt-repository \
-        "deb [arch=amd64] https://download.docker.com/linux/ubuntu \
-        $(lsb_release -cs) \
-        stable" \
-    \
-    && apt-get update -y \
-    && apt-get install -y --no-install-recommends docker-ce \
-    && rm -rf /var/lib/apt/lists/*
 
 # Install Python packages; pbr has to be installed first to workaround error in sphinxcontrib-spelling installation
 COPY requirements.txt /tmp/
@@ -228,36 +232,26 @@ RUN apt-get update -y \
         six \
     && pip${python_version_major_minor} install -U git+https://github.com/jjhelmus/CyLP.git@py3#egg=cylp \
     && pip${python_version_major_minor} install -r /tmp/requirements.txt \
-    && rm tmp/requirements.txt \
-    \
-    && apt-get remove -y \
-        build-essential \
-        swig \
-    && apt-get autoremove -y \
-    && rm -rf /var/lib/apt/lists/*
+    && rm tmp/requirements.txt 
 
 # Install NCBI taxonomy database and ETE3 package
 RUN pip${python_version_major_minor} install ete3 \
     && python${python_version_major_minor} -c "import ete3; ete3.NCBITaxa().get_descendant_taxa('Homo');" \
     && rm /taxdump.tar.gz
 
 # Save image tag to file so it is accessible from within containers
-ARG image_tag='0.2'
+ARG image_tag={{ image_tag }}
 RUN echo ${image_tag} > /etc/docker-image-tag
 
 # install debugging utilities
 RUN apt-get update -y \
-   && apt-get install -y --no-install-recommends \
-      nano \
-      postgresql \
-      snapd \
-   && snap install pycharm-community --classic \
-   && rm -rf /var/lib/apt/lists/*
+    && apt-get install -y --no-install-recommends \
+        nano 
 
 # cleanup
 RUN apt-get remove -y \
-      build-essential \
-      cmake
+    build-essential \
+    cmake
 
 # final command
 WORKDIR /root

wc_env_manager/config/core.default.cfg

@@ -1,9 +1,9 @@
 [wc_env_manager]
     # other options
-    verbose = False
+    verbose = True
 
     [[base_image]]
-        repo_unsquashed = ''
+        repo_unsquashed = lzy7071/karrlabdatanator_dependencies_unsquashed
         repo = lzy7071/karrlabdatanator_dependencies
         tags = 'latest', '0.2'
         dockerfile_template_path = ${ROOT}/assets/base_image/Dockerfile.template
@@ -13,8 +13,8 @@
             timezone = America/New_York
 
             # docker
-            docker_install = ''
-            circleci_install = ''
+            # docker_install = False
+            # circleci_install = False
 
             # Python
             python_version = 3.6.8
@@ -29,57 +29,34 @@
             curl_install = True
 
             # databases
-            postgresql_client_install = ''
+            # postgresql_client_install = False
 
             # optimization solvers
-            cbc_version = 2.8.5 # latest version compatible with CyLP
-            cbc_install = ''
-            coin_utils_version = 2.10.14
-            coin_utils_install = ''
-            cplex_version = 12.8.0
-            cplex_install = ''
-            gurobi_version = 8.1.0
-            gurobi_license = ''
-            gurobi_install = False
-            marvin_version = 19.7
-            marvin_install = True
-            minos_version = 5.6
-            minos_install = ''
-            mosek_version = 8.1.0.78
-            mosek_install = False
-            mosek_license = ''
-            qpoases_version = 3.2.1
-            qpoases_install = ''
-            soplex_version = 3.1.1 # newer version not yet supported by soplex_cython
-            soplex_install = ''
-            xpress_version = 8.5.6
-            xpress_install = ''
-            xpress_license = ''
-            xpress_license_server = ''
+
 
             # ODE solvers
-            sundials_install = ''
-            sundials_version = 3.2.1
+            # sundials_install = False
+            # sundials_version = 3.2.1
 
             # chemoinformatics tools
             openbabel_version = 2.4.1
             openbabel_install = True
 
             # bioinformatics tools
-            kallisto_version = 0.45.1
-            kallisto_install = ''
+            # kallisto_version = 0.45.1
+            # kallisto_install = False
 
     [[image]]
-        repo = lzy7071/karrlabdatanator_dependencies
+        repo = lzy7071/karrlabdatanator
         tags = 'latest', '0.2'
         dockerfile_template_path = ${ROOT}/assets/image/Dockerfile.template
         config_path = ${HOME}/.wc/
         ssh_key_path = /root/.ssh/id_rsa
         python_version = 3.6
         python_packages = '''
             # development tools
-            # ipython
-            # jupyter
+            ipython
+            jupyter
 
             # static analysis
             pylint
@@ -139,15 +116,9 @@
                     POSTGRES_USER = postgres
 
     [[container]]
-        name_format = wc_env-%Y-%m-%d-%H-%M-%S
+        name_format = datanator-%Y-%m-%d-%H-%M-%S
         python_packages = ''
-        setup_script = '''
-            if [ -x "$$(command -v datanator)" ]; then
-                datanator db create
-                datanator db migrate
-                datanator db restore --restore-schema --do-not-exit-on-error
-            fi
-            '''
+        setup_script = ''
 
     [[docker_hub]]
         # username = None