Notes

validation/Dockerfile

@@ -79,10 +79,8 @@ COPY --chmod=755 get-mmcif-dict-versions.py \
 ## day, in case something goes wrong.
 ## Dictionaries do not change that frequently therefore we skip the hassle of
 ## keeping them in an external volume.
-## To explore development versions of the MAX/mmCIF dictionary, right out of
-## the Git repo, build with USE_DICT_RELEASE="dev". Default is "master" which
-## loads from the master branch at https://github.com/ihmwg/ModelCIF.
 ARG DICT_FETCH_DATE="2022-05-02.1"
+# ToDo: use commit instead of USE_DICT_RELEASE
 ARG USE_DICT_RELEASE="master"
 ENV DICT_FETCH_DATE=${DICT_FETCH_DATE}
 ENV USE_DICT_RELEASE=${USE_DICT_RELEASE}

validation/README.md

@@ -97,11 +97,15 @@ $
 The call to the validation tool (almost) stays the same, it just needs instructions to start the Docker container as a prefix:
 
 ```bash
-$ docker run --rm -i -v /home/user/models:/data -t registry.scicore.unibas.ch/schwede/mabakerimport/mmcif-dict-suite:dev validate-mmcif-file /data/model.cif
+$ docker run --rm -v /home/user/models:/data registry.scicore.unibas.ch/schwede/mabakerimport/mmcif-dict-suite:dev validate-mmcif-file /data/model.cif
 {"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.358","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.0","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/dist/mmcif_ma.dic"}]}
 $ 
 ```
 
+`docker run` is the call to execute a certain command inside a container. `--rm` makes sure that the container is removed from the system once the job completed.
+
+Since the container has its own internal file system separated, `-v` is utilised to mount a directory from the host into the container.
+
 - explain what command does
 - explain volumes/ external mounts
 - explain for -e