Bug #14429: [CWL] Initial work dir error - Arvados

Actions

Copy link

Bug #14429

open

[CWL] Initial work dir error

Added by Jiayong Li about 6 years ago. Updated 10 months ago.

Status:

New

Priority:

Normal

Assigned To:

Category:

Target version:

Future

Story points:

Release:

Postponed

Release relationship:

Auto

Description

I used the following simple cwl to do gzip using initial work dir.

gzip.cwl

cwlVersion: v1.0
class: CommandLineTool
requirements:
  DockerRequirement:
    dockerPull: arvados/jobs
  InitialWorkDirRequirement:
    listing:
      - $(inputs.infile)
inputs:
  infile: File
outputs:
  outfile:
    type: File
    outputBinding:
      glob: "*.gz" 
baseCommand: gzip
arguments:
  - $(inputs.infile.basename)

Run: https://workbench.e51c5.arvadosapi.com/container_requests/e51c5-xvhdp-uzdzlsqwwodcz0e

Error message:

gzip: foo: Device or resource busy

Actions

Copy link

Updated by Jiayong Li about 6 years ago

Status changed from New to In Progress

Actions

Copy link

Updated by Jiayong Li about 6 years ago

Description updated (diff)
Status changed from In Progress to New

Actions

Copy link

Updated by Peter Amstutz about 6 years ago

requirements:
  DockerRequirement:
    dockerPull: arvados/jobs
  InitialWorkDirRequirement:
    listing:
      - entry: $(inputs.infile)
        writable: true

Actions

Copy link