11 add vtls dockerstack (#12)

* Add VTLS Dockerfile and udates to docker-compose.yml
* Fixed a few bugs in the vtls_dev/Dockerfile

---------

Authored-by: Godwin Shen

Author: GodwinShen

docker-compose.yml

@@ -1,6 +1,12 @@
 # ${DOCKER_GROUP} and ${DOCKER_TAG} default values defined in the .env file 
 version: '3'
 services:
+    vtls_dev:
+        image: ${DOCKER_GROUP}/vtls_dev:${DOCKER_TAG}
+        hostname: local
+        build:
+            context: ./
+            dockerfile: $PWD/vtls_dev/Dockerfile
     sounder_sips_dev:
         image: ${DOCKER_GROUP}/sounder_sips_dev:${DOCKER_TAG}
         hostname: local

vtls_dev/Dockerfile

@@ -0,0 +1,28 @@
+FROM jupyter/datascience-notebook
+
+# Switch to root user for build
+USER root
+
+# Requires the build context to be one level up where common is located
+COPY common/unity-sds /etc/unity-sds
+
+# Install Dockstore
+RUN apt-get update -q && \
+    apt install -y openjdk-11-jdk && \
+    curl -L -o /usr/local/bin/dockstore https://github.com/dockstore/dockstore-cli/releases/download/1.13.1/dockstore && \
+    chmod +x /usr/local/bin/dockstore
+
+# Install AWS CLI
+RUN curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" && \
+    unzip awscliv2.zip && \
+    ./aws/install --bin-dir /usr/local/bin --install-dir /usr/local/aws-cli && \
+    rm -rf awscliv2.zip aws
+
+RUN mamba install -y python>3.11 nb_conda_kernels ipykernel \
+        s3fs boto3 netcdf4 xarray basemap cartopy h5netcdf 'basemap>=1.4.0' pysqlite3 \
+        ipython numpy pandas matplotlib scipy && \
+    conda clean -y --all 
+RUN pip install unity_sds_client==0.7.0 podaac-data-subscriber PyWavelets
+
+# Switch back to jovyan to avoid accidental container runs as root
+USER ${NB_UID}