The Yaml Command Line Validator Tool is used to verify that a .dockstore.yml file is valid for use in Dockstore and that all referenced files are present.
I want to use the yaml (
.dockstore.yml) validation tool.
dockstore yaml validate --path directory/of/.dockstore.yml
However, I don’t see the
dockstore yaml command with the
dockstore CLI on my Fedora Linux 36. Could you tell me how to use it? Thank you.
$ java --version openjdk 17.0.4 2022-07-19 OpenJDK Runtime Environment (Red_Hat-18.104.22.168.8-1.fc36) (build 17.0.4+8) OpenJDK 64-Bit Server VM (Red_Hat-22.214.171.124.8-1.fc36) (build 17.0.4+8, mixed mode, sharing) $ dockstore --version Current version : 1.12.0 You have the most recent stable release. If you wish to upgrade to the latest unstable version, please use the following command: dockstore --upgrade-unstable Dockstore version 1.12.0 You are running the latest stable version... If you wish to upgrade to the latest unstable version, please use the following command: dockstore --upgrade-unstable
$ ls .dockstore.yml .dockstore.yml $ dockstore yaml validate --path . Current version : 1.12.0 You have the most recent stable release. If you wish to upgrade to the latest unstable version, please use the following command: dockstore --upgrade-unstable 20:01:50.647 [main] ERROR io.dockstore.client.cli.ArgumentUtility - dockstore: yaml is not a dockstore command. See 'dockstore --help'.
Edit: Perhaps the commit Feature/dock 2129/yaml file check (#161) · dockstore/dockstore-cli@033e5b7 · GitHub available from the version 1.13.0-rc.0 enables the
dockstore yaml command?
I found a tool to validate only a WDL file, as it is not an alternative of the
dockstore yaml validate command.
$ wget https://github.com/broadinstitute/cromwell/releases/download/84/womtool-84.jar $ java -jar womtool-84.jar validate /path/to/something.wdl
develop documentation refers to 1.13 which we’re currently working on and has not officially been released. You can experiment with the jar from https://artifacts.oicr.on.ca/artifactory/webapp/#/artifacts/browse/tree/General/collab-release/io/dockstore/dockstore-client/1.13.0-rc.0/dockstore-client-1.13.0-rc.0-shaded.jar but this isn’t officially supported.
Though I am not sure the difference between
dockstore-client-1.13.0-rc.0-shaded.jar there. I will try to run the
dockstore-client-1.13.0-rc.0.jar from the
dockstore shell script.
You want the
shaded one actually. That said, I’ve uploaded the files in Releasing the dockstore CLI version 1.13.0-rc.0 - #2 by dyuen so you should be able to use the
Yeah, when I just only put the
dockstore-client-1.13.0-rc.0.jar to the
~/.dockstore/self-installs/ and modified the
dockstore shell script a bit manually, I saw a kind of runtime error by
$ bash -x ./dockstore-1.13.0-rc.0 ... + java io.dockstore.client.cli.Client Error: Unable to initialize main class io.dockstore.client.cli.Client
Thanks! Yes, tried it now, and works very well!
$ dockstore --upgrade-unstable $ dockstore --version Dockstore version 1.13.0-rc.0 The latest stable version is 1.12.0 You are currently on the latest unstable version. If you wish to upgrade to the latest stable version, please use the following command: dockstore --upgrade-stable $ cd /path/to/directory $ dockstore yaml validate --path . ./.dockstore.yml is a valid yaml file ./.dockstore.yml is a valid dockstore yaml file and all required files are present $ echo $? 0