Merge pull request PecanProject#3042 from infotroph/docker-tweaks

Docker tweaks

DEV-INTRO.md

@@ -245,7 +245,7 @@ You can submit your workflow either in the executor container or in rstudio cont
 docker-compose exec executor bash
 # inside the container
 cd /pecan/tests
-R CMD ../web/workflow.R docker.sipnet.xml
+R CMD ../web/workflow.R --settings docker.sipnet.xml
 ```
 
 A better way of doing this is developed as part of GSOC, in which case you can leverage of the restful interface defined, or using the new R PEcAn API package.
@@ -310,7 +310,7 @@ If you want to reset the pecan lib folder that is mounted across all machines, f
 
 ```
 docker-compose down
-docker rm pecan_lib
+docker volume rm pecan_lib
 ```
 
 ## Linux and User permissions

docker-compose.dev.yml

@@ -8,7 +8,7 @@ services:
 
   # web application. This expects the config.php to be copied from docker/web
   # cp docker/web/config.docker.php web/config.php
-  #web:
+  #pecan:
   #  volumes:
   #    - 'pecan_web:/var/www/html/pecan'
 

docker/base/Dockerfile

@@ -23,7 +23,13 @@ COPY base     /pecan/base/
 COPY modules  /pecan/modules/
 COPY models   /pecan/models/
 
-RUN cd /pecan && make && rm -rf /tmp/downloaded_packages
+# install all PEcAn packages
+# `make clean` is to remove artifacts copied in from host system
+#   (e.g. basgra.so)
+RUN cd /pecan \
+    && make clean \
+    && make \
+    && rm -rf /tmp/downloaded_packages
 
 # COPY WORKFLOW
 WORKDIR /work

docker/docker-compose.example.yml

@@ -7,7 +7,7 @@ services:
 
   # mount PEcAn web folder into web server, this allows for
   # editing code in PHP and immediatly test the new code.
-  web:
+  pecan:
     volumes:
       - ${HOME}/git/pecan/web:/var/www/html/pecan
       - ${HOME}/git/pecan/docker/config.docker.php:/var/www/html/pecan/config.php