icgc-storage-client-plugin

Dockstore icgc score client file provisioning plugin. With the closure of the ICGC data portal, this repository is now archived.

Usage

The icgc score client plugin is capable of downloading files by calling out to a Docker image of the icgc-score-client. Currently it has only been tested with downloading a directory of files from icgc.

$ cat dockstore.wdl 
task stat {
  File dir
  command {
    stat ${dir}
  }
  output {
    String outf = read_string(stdout())
  }
}
workflow dir_check {
  call stat
}

$ cat dockstore.json
{
  "dir_check.stat.dir": "icgc://eeca3ccd-fa4e-57bf-9fde-c9d0ddf69935"
}

$ dockstore workflow launch --local-entry dockstore.wdl --json dockstore.json
Creating directories for run of Dockstore launcher in current working directory: /home/user/testCLI
Provisioning your input files to your local machine
Downloading: dir_check.stat.dir from icgc://eeca3ccd-fa4e-57bf-9fde-c9d0ddf69935 to: /home/user/testCLI/cromwell-input/1ad7fb3d-62bc-4e1a-8d5d-cc173c0d4e82/icgc:/eeca3ccd-fa4e-57bf-9fde-c9d0ddf69935
Calling on plugin io.dockstore.provision.ICGCStorageClientPlugin$ICGCStorageClientProvision to provision icgc://eeca3ccd-fa4e-57bf-9fde-c9d0ddf69935
...

Configuration

This plugin gets configuration information from the following structure in ~/.dockstore/config

[dockstore-file-icgc-storage-client-plugin]
client-key = ########-####-####-####-############

Docker will need to be installed