Merge pull request #17 from broadinstitute/ab_docker_install_script

Added new install.sh script for consistent dependencies...

.git_ignore

@@ -4,7 +4,8 @@ entity_update.tsv
 __pycache__/
 *.py[cod]
 *$py.class
-
+scripts/*.py[cod]
+scripts/*$py.class
 # Environments
 .env
 .venv
@@ -13,4 +14,6 @@ venv/
 ENV/
 
 # IntelliJ
-**/.idea/
\ No newline at end of file
+**/.idea/
+
+.firecloud-tools

Dockerfile

 FROM google/cloud-sdk:170.0.1-slim
 
-RUN pip install virtualenv
-RUN virtualenv -q ~/.firecloud-tools/venv
-RUN /bin/bash -c "source ~/.firecloud-tools/venv/bin/activate"
+COPY install.sh /
+RUN /install.sh
 	
-RUN pip install --upgrade pip
-
-RUN pip install PyYAML google-cloud-datastore google-cloud google-auth-httplib2 google-api-python-client gcs-oauth2-boto-plugin \
-retrying firecloud xlrd google-cloud-bigquery google-cloud-logging pandas
-
 # Tell gcloud to save state in /.config so it's easy to override as a mounted volume.
 ENV HOME=/
 

install.sh

+pip install --upgrade pip
+pip install PyYAML
+pip install google-auth-httplib2
+pip install google-api-python-client
+pip install gcs-oauth2-boto-plugin
+pip install google-cloud-datastore
+pip install google-cloud
+pip install retrying
+pip install firecloud
+pip install xlrd
+pip install --upgrade google-cloud-bigquery==0.27
+pip install pandas

run.sh

+set -e
 cd "$(dirname "$0")"
-
 # only do the setup if it has not already been done
-if [ ! -d ~/.firecloud-tools ]; then
+if [ ! -d .firecloud-tools ]; then
   	# add conditionals to only do if not existing
 	pip install virtualenv
 
-	virtualenv -q ~/.firecloud-tools/venv
-	
-	source ~/.firecloud-tools/venv/bin/activate
+	virtualenv -q .firecloud-tools/venv
 	
-	pip install --upgrade pip
-	pip install PyYAML
-	pip install google-auth-httplib2
-	pip install google-api-python-client
-	pip install gcs-oauth2-boto-plugin
-	pip install retrying
-	pip install firecloud
-	pip install xlrd
-	pip install --upgrade google-cloud-bigquery
-	pip install pandas
-	#pip install .
+    source .firecloud-tools/venv/bin/activate
+    ./install.sh
 fi
 
-export PYTHONPATH=./:$PYTHONPATH
-source ~/.firecloud-tools/venv/bin/activate
-
-python -u $@
\ No newline at end of file
+source .firecloud-tools/venv/bin/activate
+export PYTHONPATH=./:scripts:$PYTHONPATH
+python -u $@