Merge pull request #314 from alan-turing-institute/DSG-APR2019-Deployment

Merge changes from April DSG

Author: jemrobinson

.gitignore

@@ -1,7 +1,7 @@
 # System files
 *.DS_Store
 .idea/
-logistic.csv
+new_dsg_environment/azure-vms/tests/logistic.csv
 
 # All secrets folders, no matter how nested
 secrets/

new_dsg_environment/azure-vms/DSG_configs/cloud-init-compute-vm-DSG-10.yaml

@@ -167,16 +167,12 @@ runcmd:
   - cp /Rprofile.site /anaconda/envs/py36/lib/R/etc/Rprofile.site
   - cp /Rprofile.site /anaconda/envs/py37/lib/R/etc/Rprofile.site
   # Create shared data folder and grant all users access
+  - echo "Creating shared data folder"
   - sudo mkdir /data
   - sudo chmod go+rw /data
   # Make sure that sssd is running
   - echo "Restart sssd service"
   - service sssd restart
-  # Give anaconda directory to plugdev group (which all new users are a part of) and set group permissions equal to user
-  - echo "Change ownership of /anaconda/"
-  - chgrp -R plugdev /anaconda/
-  - chmod -R g=u /anaconda/
-  - chmod -R go-w /anaconda/
   # Set py36 as default environment when launching a new shell
   - echo "Add py36 conda environment setup to global bashrc"
   - echo "conda activate py36" >> /etc/bash.bashrc

new_dsg_environment/azure-vms/DSG_configs/cloud-init-compute-vm-DSG-11.yaml

@@ -167,16 +167,12 @@ runcmd:
   - cp /Rprofile.site /anaconda/envs/py36/lib/R/etc/Rprofile.site
   - cp /Rprofile.site /anaconda/envs/py37/lib/R/etc/Rprofile.site
   # Create shared data folder and grant all users access
+  - echo "Creating shared data folder"
   - sudo mkdir /data
   - sudo chmod go+rw /data
   # Make sure that sssd is running
   - echo "Restart sssd service"
   - service sssd restart
-  # Give anaconda directory to plugdev group (which all new users are a part of) and set group permissions equal to user
-  - echo "Change ownership of /anaconda/"
-  - chgrp -R plugdev /anaconda/
-  - chmod -R g=u /anaconda/
-  - chmod -R go-w /anaconda/
   # Set py36 as default environment when launching a new shell
   - echo "Add py36 conda environment setup to global bashrc"
   - echo "conda activate py36" >> /etc/bash.bashrc

new_dsg_environment/azure-vms/DSG_configs/cloud-init-compute-vm-DSG-12.yaml

@@ -167,16 +167,12 @@ runcmd:
   - cp /Rprofile.site /anaconda/envs/py36/lib/R/etc/Rprofile.site
   - cp /Rprofile.site /anaconda/envs/py37/lib/R/etc/Rprofile.site
   # Create shared data folder and grant all users access
+  - echo "Creating shared data folder"
   - sudo mkdir /data
   - sudo chmod go+rw /data
   # Make sure that sssd is running
   - echo "Restart sssd service"
   - service sssd restart
-  # Give anaconda directory to plugdev group (which all new users are a part of) and set group permissions equal to user
-  - echo "Change ownership of /anaconda/"
-  - chgrp -R plugdev /anaconda/
-  - chmod -R g=u /anaconda/
-  - chmod -R go-w /anaconda/
   # Set py36 as default environment when launching a new shell
   - echo "Add py36 conda environment setup to global bashrc"
   - echo "conda activate py36" >> /etc/bash.bashrc

new_dsg_environment/azure-vms/DSG_configs/cloud-init-compute-vm-DSG-13.yaml

@@ -167,16 +167,12 @@ runcmd:
   - cp /Rprofile.site /anaconda/envs/py36/lib/R/etc/Rprofile.site
   - cp /Rprofile.site /anaconda/envs/py37/lib/R/etc/Rprofile.site
   # Create shared data folder and grant all users access
+  - echo "Creating shared data folder"
   - sudo mkdir /data
   - sudo chmod go+rw /data
   # Make sure that sssd is running
   - echo "Restart sssd service"
   - service sssd restart
-  # Give anaconda directory to plugdev group (which all new users are a part of) and set group permissions equal to user
-  - echo "Change ownership of /anaconda/"
-  - chgrp -R plugdev /anaconda/
-  - chmod -R g=u /anaconda/
-  - chmod -R go-w /anaconda/
   # Set py36 as default environment when launching a new shell
   - echo "Add py36 conda environment setup to global bashrc"
   - echo "conda activate py36" >> /etc/bash.bashrc

new_dsg_environment/azure-vms/DSG_configs/cloud-init-compute-vm-DSG-14.yaml

@@ -167,16 +167,12 @@ runcmd:
   - cp /Rprofile.site /anaconda/envs/py36/lib/R/etc/Rprofile.site
   - cp /Rprofile.site /anaconda/envs/py37/lib/R/etc/Rprofile.site
   # Create shared data folder and grant all users access
+  - echo "Creating shared data folder"
   - sudo mkdir /data
   - sudo chmod go+rw /data
   # Make sure that sssd is running
   - echo "Restart sssd service"
   - service sssd restart
-  # Give anaconda directory to plugdev group (which all new users are a part of) and set group permissions equal to user
-  - echo "Change ownership of /anaconda/"
-  - chgrp -R plugdev /anaconda/
-  - chmod -R g=u /anaconda/
-  - chmod -R go-w /anaconda/
   # Set py36 as default environment when launching a new shell
   - echo "Add py36 conda environment setup to global bashrc"
   - echo "conda activate py36" >> /etc/bash.bashrc

new_dsg_environment/azure-vms/DSG_configs/cloud-init-compute-vm-DSG-15.yaml

@@ -167,16 +167,12 @@ runcmd:
   - cp /Rprofile.site /anaconda/envs/py36/lib/R/etc/Rprofile.site
   - cp /Rprofile.site /anaconda/envs/py37/lib/R/etc/Rprofile.site
   # Create shared data folder and grant all users access
+  - echo "Creating shared data folder"
   - sudo mkdir /data
   - sudo chmod go+rw /data
   # Make sure that sssd is running
   - echo "Restart sssd service"
   - service sssd restart
-  # Give anaconda directory to plugdev group (which all new users are a part of) and set group permissions equal to user
-  - echo "Change ownership of /anaconda/"
-  - chgrp -R plugdev /anaconda/
-  - chmod -R g=u /anaconda/
-  - chmod -R go-w /anaconda/
   # Set py36 as default environment when launching a new shell
   - echo "Add py36 conda environment setup to global bashrc"
   - echo "conda activate py36" >> /etc/bash.bashrc

new_dsg_environment/azure-vms/DSG_configs/cloud-init-compute-vm-DSG-4.yaml

@@ -175,11 +175,6 @@ runcmd:
   # Make sure that sssd is running
   - echo "Restart sssd service"
   - service sssd restart
-  # Give anaconda directory to plugdev group (which all new users are a part of) and set group permissions equal to user
-  - echo "Change ownership of /anaconda/"
-  - chgrp -R plugdev /anaconda/
-  - chmod -R g=u /anaconda/
-  - chmod -R go-w /anaconda/
   # Set py36 as default environment when launching a new shell
   - echo "Add py36 conda environment setup to global bashrc"
   - echo "source activate py36" >> /etc/bash.bashrc

new_dsg_environment/azure-vms/DSG_configs/cloud-init-compute-vm-DSG-9.yaml

@@ -167,16 +167,12 @@ runcmd:
   - cp /Rprofile.site /anaconda/envs/py36/lib/R/etc/Rprofile.site
   - cp /Rprofile.site /anaconda/envs/py37/lib/R/etc/Rprofile.site
   # Create shared data folder and grant all users access
+  - echo "Creating shared data folder"
   - sudo mkdir /data
   - sudo chmod go+rw /data
   # Make sure that sssd is running
   - echo "Restart sssd service"
   - service sssd restart
-  # Give anaconda directory to plugdev group (which all new users are a part of) and set group permissions equal to user
-  - echo "Change ownership of /anaconda/"
-  - chgrp -R plugdev /anaconda/
-  - chmod -R g=u /anaconda/
-  - chmod -R go-w /anaconda/
   # Set py36 as default environment when launching a new shell
   - echo "Add py36 conda environment setup to global bashrc"
   - echo "conda activate py36" >> /etc/bash.bashrc

new_dsg_environment/azure-vms/DSG_configs/cloud-init-compute-vm-DSG-TEST.yaml

@@ -167,16 +167,12 @@ runcmd:
   - cp /Rprofile.site /anaconda/envs/py36/lib/R/etc/Rprofile.site
   - cp /Rprofile.site /anaconda/envs/py37/lib/R/etc/Rprofile.site
   # Create shared data folder and grant all users access
+  - echo "Creating shared data folder"
   - sudo mkdir /data
   - sudo chmod go+rw /data
   # Make sure that sssd is running
   - echo "Restart sssd service"
   - service sssd restart
-  # Give anaconda directory to plugdev group (which all new users are a part of) and set group permissions equal to user
-  - echo "Change ownership of /anaconda/"
-  - chgrp -R plugdev /anaconda/
-  - chmod -R g=u /anaconda/
-  - chmod -R go-w /anaconda/
   # Set py36 as default environment when launching a new shell
   - echo "Add py36 conda environment setup to global bashrc"
   - echo "conda activate py36" >> /etc/bash.bashrc