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Badge](https://app.codacy.com/project/badge/Grade/c583635906d84de5a1b5f62068fc26be)](https://www.codacy.com/gh/dockstore/dockstore-cli/dashboard?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=dockstore/dockstore-cli\u0026amp;utm_campaign=Badge_Grade)\n[![codecov](https://codecov.io/gh/dockstore/dockstore-cli/branch/master/graph/badge.svg)](https://codecov.io/gh/dockstore/dockstore-cli)\n[![Website](https://img.shields.io/website/https/dockstore.org.svg)](https://dockstore.org)\n[![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/ga4gh/dockstore?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge\u0026utm_content=badge)  \n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2630727.svg)](https://doi.org/10.5281/zenodo.2630727)\n[![license](https://img.shields.io/hexpm/l/plug.svg?maxAge=2592000)](LICENSE)\n[![CircleCI](https://circleci.com/gh/dockstore/dockstore-cli/tree/develop.svg?style=svg)](https://circleci.com/gh/dockstore/dockstore-cli/tree/develop)\n[![Documentation Status](https://readthedocs.org/projects/dockstore/badge/?version=develop)](https://dockstore.readthedocs.io/en/develop/?badge=develop)\n\n\n# Dockstore\n\nDockstore provides a place for users to share tools encapsulated in Docker and described with the Common \nWorkflow Language (CWL), WDL (Workflow Description Language), or Nextflow. This enables scientists to share analytical \nworkflows so that they are  machine readable as well as runnable in a variety of environments. While the \nDockstore is focused on serving researchers in the biosciences, the combination of Docker + CWL/WDL can be used by \nanyone to describe the tools and services in their Docker images in a standardized, machine-readable way.  \nWe hope to use this project as motivation to create a GA4GH API standard for container registries.\n\nFor the live site see [dockstore.org](https://dockstore.org)\n\nThis repo contains the CLI components for Dockstore  \n\nFor the main repo see [dockstore](https://github.com/dockstore/dockstore).\nFor the related web UI see [dockstore-ui](https://github.com/dockstore/dockstore-ui2).\n\n## For Dockstore Users\n\nThe following section is useful for users of Dockstore (e.g. those that want to browse, register, and \nlaunch tools). \n\nAfter registering at [dockstore.org](https://dockstore.org), you will be able to download the Dockstore \nCLI at [onboarding](https://dockstore.org/onboarding). The Dockstore command line script should be installed in a location in your path.\n\n### Configuration File\n\nA basic Dockstore configuration file is available/should be created in `~/.dockstore/config` and contains the following\nat minimum:\n```\ntoken = \u003cyour generated by the dockstore site\u003e\nserver-url = https://www.dockstore.org/api\n```\n\nFor 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`.\n\nAs 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\n\n```\ntokenCommand = cat /home/my-user/dockstoreTokenVault.txt\nserver-url = https://www.dockstore.org/api\n```\n\n### File Provisioning\n\nBy default, cwltool reads input files from the local filesystem. Dockstore also adds support for additional file systems\nsuch as http, https, and ftp. Through a plug-in system, Dockstore also supports \nAmazon S3 and [Synapse](https://help.synapse.org/docs/Downloading-Data-Programmatically.2003796248.html) via [plugins](https://github.com/dockstore).\n\nDownload the above set of default plugins via: \n```\ndockstore plugin download\n```\n\nConfiguration for plugins can be placed inside the Dockstore configuration file in the following format\n\n```\ntoken = \u003cyour generated by the dockstore site\u003e\nserver-url = https://www.dockstore.org/api\n\n# options below this are optional\n\nuse-cache = false                           #set this to true to cache input files for rapid development\ncache-dir = /home/\u003cuser\u003e/.dockstore/cache   #set this to determine where input files are cached (should be the same filesystem as your tool working directories)\n\n[dockstore-file-synapse-plugin]\n\n[dockstore-file-s3-plugin]\nendpoint = #set this to point at a non AWS S3 endpoint\n```\n\nAdditional plugins can be created by taking one of the repos in [plugins](https://github.com/dockstore) as a model and \nusing [pf4j](https://github.com/decebals/pf4j) as a reference. See [additional documentation](dockstore-file-plugin-parent) for more details. \n\n## Development\n\n### Coding Standards\n\n[codestyle.xml](codestyle.xml) defines the coding style for Dockstore as an IntelliJ Code Style XML file that should be imported into IntelliJ IDE. \nWe also have a matching [checkstyle.xml](checkstyle.xml) that can be imported into other IDEs and is run during the build.  \n\nFor 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. \n\n### Dockstore Command Line\n\nBe sure to have a configuration file in place. Follow the instructions in [Configuration File](#configuration-file) for help.\n\nAdd the directory `dockstore-client/bin` to your PATH: \n\n```bash\n  cd dockstore-cli \n  echo \"export PATH=$(pwd)/dockstore-client/bin:\"'$PATH' \u003e\u003e ~/.bash_profile\n  source ~/.bash_profile\n```\n\nIf you are working with a custom-built or updated dockstore client you will need to update the jar in: `~/.dockstore/self-installs`.\n\n### Encrypted Documents for Travis-CI\n\nEncrypted documents necessary for confidential testing are handled as indicated in the documents at Travis-CI for  \n[files](https://docs.travis-ci.com/user/encrypting-files/#Encrypting-multiple-files) and [environment variables](https://docs.travis-ci.com/user/encryption-keys).\n\nA 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. \n\n### Adding Copyright header to all files with IntelliJ\n\nTo add copyright headers to all files with IntelliJ\n\n1. Ensure the Copyright plugin is installed (Settings -\u003e Plugins)\n2. Create a new copyright profile matching existing copyright header found on all files, name it Dockstore (Settings -\u003e Copyright -\u003e Copyright Profiles -\u003e Add New)\n3. Set the default project copyright to Dockstore (Settings -\u003e Copyright)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdockstore%2Fdockstore-cli","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdockstore%2Fdockstore-cli","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdockstore%2Fdockstore-cli/lists"}