From e5d1bda1dc81e99cf46a45a1ca5345d789435318 Mon Sep 17 00:00:00 2001
From: B13nch3n <b13nch3n_01@theb-si.de>
Date: Tue, 10 May 2022 21:59:43 +0200
Subject: [PATCH] Notes
---
validation/Dockerfile | 4 +---
validation/README.md | 6 +++++-
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/validation/Dockerfile b/validation/Dockerfile
index 062c0c4..e9022a1 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 769ce3c..5f6407c 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
--
GitLab