ABS-64; more docker dependencies

docker/anaconda3_neuron_1370/Dockerfile

@@ -9,18 +9,31 @@ MAINTAINER Tim Fliss <[email protected]>
 
 # neuron installation
 WORKDIR root
-COPY shared shared
 COPY requirements.txt test_requirements.txt ./
+COPY shared shared/apt_get_dependencies.sh
 RUN /bin/bash shared/apt_get_dependencies.sh
+COPY shared shared/conda_27.sh
 RUN /bin/bash shared/conda_27.sh
+COPY shared shared/allensdk_install.sh
+RUN /bin/bash --login shared/allensdk_install.sh
+COPY shared shared/jupyterhub.sh
 RUN /bin/bash --login shared/jupyterhub.sh
+COPY shared shared/build_nrn.sh
 RUN /bin/bash --login shared/build_nrn.sh
+COPY shared shared/tensorflow.sh
 RUN /bin/bash --login shared/tensorflow.sh
+COPY shared shared/aws_dependencies.sh
+RUN /bin/bash --login shared/aws_dependencies.sh
+COPY shared shared/users.sh
 RUN /bin/bash --login shared/users.sh
 
-RUN shared/build_DiPDE.sh -e py27
+COPY shared/build_DiPDE.sh shared/
+#RUN shared/build_DiPDE.sh -e py27
+COPY shared/build_NEST.sh shared/
 RUN shared/build_NEST.sh -e py27
-RUN shared/build_NEURON.sh -e py27
+COPY shared/build_NEURON.sh shared/
+#RUN shared/build_NEURON.sh -e py27
+COPY shared/build_Tensorflow.sh shared/
 #RUN shared/build_Tensorflow.sh -e py27
 
 RUN /bin/bash shared/aws_dependencies.sh

docker/anaconda3_neuron_1370/shared/allensdk_install.sh

@@ -0,0 +1,13 @@
+cd /root
+wget https://github.com/AllenInstitute/AllenSDK/archive/v0.13.1.tar.gz
+tar xvzf v0.13.1.tar.gz
+mv AllenSDK-0.13.1 allensdk
+cd allensdk
+source activate root
+pip install --ignore-installed -r requirements.txt
+pip install --ignore-installed -r test_requirements.txt
+pip install .
+source activate py27
+pip install --ignore-installed -r requirements.txt
+pip install --ignore-installed -r test_requirements.txt
+pip install .

docker/anaconda3_neuron_1370/shared/aws_dependencies.sh

@@ -5,9 +5,13 @@ apt-get -yq install \
  libcurl4-openssl-dev \
  libxml2-dev
 
+source activate py27
+
 git clone https://github.com/s3fs-fuse/s3fs-fuse.git
 cd s3fs-fuse
 ./autogen.sh
 ./configure
 make
 make install
+
+pip install boto3 bokeh awscli

docker/anaconda3_neuron_1370/shared/conda_27.sh

@@ -1,10 +1,12 @@
-conda update anaconada
+conda update -y conada
 source activate root
 pip install -r requirements.txt
 pip install -r test_requirements.txt
 conda env create -n py27 python=2.7 -f shared/environment.yml
-conda install -n py27 -c https://conda.anaconda.org/simpleitk SimpleITK
+conda install -n py27 -y -c https://conda.anaconda.org/simpleitk SimpleITK
 source activate py27
 pip install --upgrade pip
 pip install --ignore-installed -r requirements.txt
 pip install --ignore-installed -r test_requirements.txt
+source activate root
+/opt/conda/envs/py27/bin/python -m ipykernel install

docker/aws_jupyterhub/Dockerfile

@@ -7,7 +7,7 @@ FROM alleninstitute/allensdk:anaconda3_neuron_1370
 
 MAINTAINER Tim Fliss <[email protected]>
 
-RUN conda create -n py2 python=2 anaconda
+RUN conda create -n py27 python=2.7 anaconda
 
 RUN /bin/bash --login -c "cd /root; \
     wget https://github.com/AllenInstitute/AllenSDK/archive/v0.13.1.tar.gz; \
@@ -16,10 +16,10 @@ RUN /bin/bash --login -c "cd /root; \
     cd allensdk; \
     pip install -r requirements.txt; \
     pip install -r test_requirements.txt; \
-    pip install .; \sou
+    pip install .; \
     ipython kernel install; \
     source activate root; \
-    /opt/conda/envs/py2/bin/python -m ipykernel install"
+    /opt/conda/envs/py27/bin/python -m ipykernel install"
 
 
 RUN apt-get install -y npm vim; \