https://github.com/dockstore/dockstore-cli
Command-line interface to dockstore, split out from main repo in version 1.8.0
https://github.com/dockstore/dockstore-cli
Last synced: 5 months ago
JSON representation
Command-line interface to dockstore, split out from main repo in version 1.8.0
- Host: GitHub
- URL: https://github.com/dockstore/dockstore-cli
- Owner: dockstore
- License: apache-2.0
- Created: 2019-09-11T20:23:28.000Z (almost 7 years ago)
- Default Branch: develop
- Last Pushed: 2025-10-16T15:57:53.000Z (8 months ago)
- Last Synced: 2025-10-16T20:42:27.628Z (8 months ago)
- Language: Java
- Homepage: https://dockstore.org
- Size: 20.6 MB
- Stars: 4
- Watchers: 2
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION
- Support: support/findbugs-exclude.xml
Awesome Lists containing this project
README
[](https://www.codacy.com/gh/dockstore/dockstore-cli/dashboard?utm_source=github.com&utm_medium=referral&utm_content=dockstore/dockstore-cli&utm_campaign=Badge_Grade)
[](https://codecov.io/gh/dockstore/dockstore-cli)
[](https://dockstore.org)
[](https://gitter.im/ga4gh/dockstore?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
[](https://doi.org/10.5281/zenodo.2630727)
[](LICENSE)
[](https://circleci.com/gh/dockstore/dockstore-cli/tree/develop)
[](https://dockstore.readthedocs.io/en/develop/?badge=develop)
# 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](https://dockstore.org)
This repo contains the CLI components for Dockstore
For the main repo see [dockstore](https://github.com/dockstore/dockstore).
For the related web UI see [dockstore-ui](https://github.com/dockstore/dockstore-ui2).
## 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](https://dockstore.org), you will be able to download the Dockstore
CLI at [onboarding](https://dockstore.org/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 =
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](https://help.synapse.org/docs/Downloading-Data-Programmatically.2003796248.html) via [plugins](https://github.com/dockstore).
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](https://github.com/dockstore) as a model and
using [pf4j](https://github.com/decebals/pf4j) as a reference. See [additional documentation](dockstore-file-plugin-parent) for more details.
## Development
### Coding Standards
[codestyle.xml](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](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](#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](https://docs.travis-ci.com/user/encrypting-files/#Encrypting-multiple-files) and [environment variables](https://docs.travis-ci.com/user/encryption-keys).
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](https://github.com/dockstore/dockstore/blob/0b59791440af6e3d383d1aede1774c0675b50404/encrypt.sh#L13). 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)