Dockstore

Dockstore provides a place for users to share tools encapsulated in Docker and described with the Common Workflow Language (CWL), WDL (Workflow Description Language), or Nextflow. This enables scientists to share analytical workflows so that they are machine readable as well as runnable in a variety of environments. While the Dockstore is focused on serving researchers in the biosciences, the combination of Docker + CWL/WDL can be used by anyone to describe the tools and services in their Docker images in a standardized, machine-readable way.
We hope to use this project as motivation to create a GA4GH API standard for container registries.

For the live site see dockstore.org

This repo contains the CLI components for Dockstore

For the main repo see dockstore. For the related web UI see dockstore-ui.

For Dockstore Users

The following section is useful for users of Dockstore (e.g. those that want to browse, register, and launch tools).

After registering at dockstore.org, you will be able to download the Dockstore CLI at onboarding. The Dockstore command line script should be installed in a location in your path.

Configuration File

A basic Dockstore configuration file is available/should be created in ~/.dockstore/config and contains the following at minimum: token = <your generated by the dockstore site> server-url = https://www.dockstore.org/api

For developers, if you are working with a custom-built or updated Dockstore client you will need to update the jar in: ~/.dockstore/config/self-installs.

As an option for additional safety, you can also store your token in an encrypted password manager or similar. In this case, you can replace token with tokenCommand. For example

tokenCommand = cat /home/my-user/dockstoreTokenVault.txt server-url = https://www.dockstore.org/api

File Provisioning

By default, cwltool reads input files from the local filesystem. Dockstore also adds support for additional file systems such as http, https, and ftp. Through a plug-in system, Dockstore also supports Amazon S3 and Synapse via plugins.

Download the above set of default plugins via: dockstore plugin download

Configuration for plugins can be placed inside the Dockstore configuration file in the following format

``` token = server-url = https://www.dockstore.org/api

options below this are optional

use-cache = false #set this to true to cache input files for rapid development cache-dir = /home//.dockstore/cache #set this to determine where input files are cached (should be the same filesystem as your tool working directories)

[dockstore-file-synapse-plugin]

[dockstore-file-s3-plugin] endpoint = #set this to point at a non AWS S3 endpoint ```

Additional plugins can be created by taking one of the repos in plugins as a model and using pf4j as a reference. See additional documentation for more details.

Development

Coding Standards

codestyle.xml defines the coding style for Dockstore as an IntelliJ Code Style XML file that should be imported into IntelliJ IDE. We also have a matching checkstyle.xml that can be imported into other IDEs and is run during the build.

For users of Intellij or comparable IDEs, we also suggest loading the checkstyle.xml with a plugin in order to display warnings and errors while coding live rather than encountering them later when running a build.

Dockstore Command Line

Be sure to have a configuration file in place. Follow the instructions in Configuration File for help.

Add the directory dockstore-client/bin to your PATH:

bash cd dockstore-cli echo "export PATH=$(pwd)/dockstore-client/bin:"'$PATH' >> ~/.bash_profile source ~/.bash_profile

If you are working with a custom-built or updated dockstore client you will need to update the jar in: ~/.dockstore/self-installs.

Encrypted Documents for Travis-CI

Encrypted documents necessary for confidential testing are handled as indicated in the documents at Travis-CI for
files and environment variables.

A convenience script is provided as encrypt.sh which will compress confidential files, encrypt them, and then update an encrypted archive on GitHub. Confidential files should also be added to .gitignore to prevent accidental check-in. The unencrypted secrets.tar should be privately distributed among members of the team that need to work with confidential data. When using this script you will likely want to alter the CUSTOM_DIR_NAME. This is necessary since running the script will overwrite the existing encryption keys, instantly breaking existing builds using that key. Our current workaround is to use a new directory when providing a new bundle.

Adding Copyright header to all files with IntelliJ

To add copyright headers to all files with IntelliJ

1. Ensure the Copyright plugin is installed (Settings -> Plugins)
2. Create a new copyright profile matching existing copyright header found on all files, name it Dockstore (Settings -> Copyright -> Copyright Profiles -> Add New)
3. Set the default project copyright to Dockstore (Settings -> Copyright)