diff --git a/validation/Dockerfile b/validation/Dockerfile index 062c0c4c3bb285b634cf72d06b6809d9d7e74a3a..e9022a10b4c04836a7a2318e81799571d7051c82 100644 --- a/validation/Dockerfile +++ b/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} diff --git a/validation/README.md b/validation/README.md index 769ce3c36fc5a75d4ba3271943263383e9a56792..5f6407c1fd1bf36f67e45e142adab5efe10a0403 100644 --- a/validation/README.md +++ b/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