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The jobs file-system

BatchX maintains a read-only file-system under jobs/ to store job information.

On job submission, BatchX creates a folder at jobs/<job-id> aimed at storing the following information:

  • Image coordinates.
  • Original job input message.
  • Aliases to referenced job input files.
  • Reproducible job input message.
  • Output message.
  • Output files.

In order to view the job folder using the CLI:

  1. Make sure you have completed the CLI installation.
  2. Activate the environment the job belongs to by using thebx env command.
  3. Inspect the job folder structure by running bx treejobs/<job-id>.

Example:

$ bx tree -i jobs/1491
jobs/1491
├── [50 B] image.txt
├── input
│   ├── file0
│   │   └── [1.8 GB] L19-5849_GGCACG_L006.UMI.aligned.sorted.bam
│   ├── [193 B] input.json
│   └── [192 B] original-input.json
└── output
    ├── L19-5849.UMI.no_dups
    │   ├── [  5.3 MB] L19-5849.UMI.no_dups.bai
    │   ├── [229.0 MB] L19-5849.UMI.no_dups.bam
    │   └── [ 11.0 kB] L19-5849.UMI.no_dups.metrics.txt
    └── [62 B] output.json