split build into dev docker-compose config, and updated readme accord…

…ingly

README.md

@@ -124,6 +124,18 @@ or:
 docker-compose run --rm mrtarget --help
 ```
 
+#### development with docker-compose
+
+By default, the docker compose file will *not use a locally built image* because it will download the latest image from [quay.io/opentargets/mrtarget](https://www.quay.io/repository/opentargets/mrtarget). So any changes made will not be applied by default.
+
+Docker-compose has the ability to layer multiple docker-compose.yml files together; by default, `docker-compose.override.yml` will be added to `docker-compose.yml`. This can be used to use an override to build the image locally i.e.:
+
+```sh
+docker-compose run --rm -f docker-compose.yml -f docker-compose.dev.yml mrtarget --dry-run my-elasticsearch-prefix
+```
+
+This is done because overrides cannot remove previous values, so once a build directive has been specified it will always be used. Therefore, the build instruction must be outside of the default docker-compose.yml to support cases where the pipeline should be run but not built.
+
 ---
 ## Using the Makefile
 
@@ -178,7 +190,7 @@ It is possible to use both docker and the makefile together. You will need to ov
 docker-compose run --rm --entrypoint make mrtarget -j -l 8 -r -R -k all
 ```
 
-
+As discussed above, by default, the docker compose file will *not use a locally built image*. See above for how to work with this.
 
 
 ---

docker-compose.dev.yml

@@ -0,0 +1,6 @@
+version: "3.6"
+services:
+
+  mrtarget:
+    build:
+      context: ./

docker-compose.yml

@@ -51,6 +51,10 @@ services:
       - ELASTICSEARCH_NODES=http://elasticsearch:9200
       - CTTV_REDIS_REMOTE=true
       - CTTV_REDIS_SERVER=redis:6379
+    volumes:
+      - ./log:/usr/src/app/log
+      - ./json:/usr/src/app/json
+      - ./qc:/usr/src/app/qc
 
 volumes:
   esdata: