Environment Variables

Cloudgene supports several environment variables that can be used in your cloudgene.yaml files to get informations about the application itself and the submitted job.

Requirements

Variable Description
${hadoop_installed}
${docker_installed}
${r_markdown_installed}

Application

Variable Description
${app_local_folder} The path of the application directory.
This is the directory where your cloudgene.yaml file is located.
${app_hdfs_folder} The path of the application HDFS directory.
This is the directory where you should put meta files.
${local_app_folder} Deprecreated. Please use ${app_local_folder}
${hdfs_app_folder} Deprecreated Please use ${app_hdfs_folder}
${workdir} Deprecreated. Please use ${app_local_folder}

Job

Variable Description
${job_id} The id of the submitted job.
${job_local_output} The workspace folder of the submitted job.
${job_local_temp} The folder of the submitted job that can be used for temporary files.
After the job is completed all files within this folder are deleted automatically.
${job_hdfs_output} The workspace HDFS folder of the submitted job in.
${job_hdfs_temp} The HDFS folder of the submitted job that can be used for temporary files.
After the job is completed all files within this folder are deleted automatically.

User

Variable Description
${user_username} The username of the user who submitted the job.
${user_mail} The email address of the user who submitted the job.

Example

name: print username
version: 1.0.0
workflow:
  steps:
    - name: Say hello
        cmd: /bin/echo hey ${user_username}
        stdout: true