cwltool issue using SoftwareRequirement

Question

[sf21]

I am having trouble executing the cwl script when supplying "SoftwareRequirement" hints. Tried the below code using both modules (--beta-dependency-resolvers-configuration) and conda (--beta-conda-dependencies). The script works when I provide the complete path to the tool in baseCommand. I am not sure what I am doing wrong. Any feedback is appreciated. thanks!

Tried with cwl version: 1.0.20180809224403

Partial stack trace. The rest was just output from conda. I can update if you think its relevant.

openjdk-8.0.12 100% |##############################################################| Time: 0:00:01  59.85 MB/s
rtg-tools-3.8. 100% |##############################################################| Time: 0:00:00  15.25 MB/s
Extracting packages ...
[      COMPLETE      ]|#################################################################################| 100%
Linking packages ...
[      COMPLETE      ]|#################################################################################| 100%
#
# To activate this environment, use:
# > source activate __rtg-tools@3.8.2
#
# To deactivate this environment, use:
# > source deactivate __rtg-tools@3.8.2
#

Exception while running job
Traceback (most recent call last):
  File "/nethome/usevani/miniconda2/lib/python2.7/site-packages/cwltool/job.py", line 278, in _execute
    name=self.name
  File "/nethome/usevani/miniconda2/lib/python2.7/site-packages/cwltool/job.py", line 575, in _job_popen
    mode="wb") as job_file:
ValueError: binary mode doesn't take an encoding argument
[job rtg.cwl] completed permanentFail
{}
Final process status is permanentFail

CWL script.

cwlVersion: v1.0
class: CommandLineTool
baseCommand: rtg

requirements:
  EnvVarRequirement:
    envDef:
      TOIL_GRIDENGINE_PE: smp

hints:
  SoftwareRequirement:
    packages:
    - package: 'rtg'
      version:
      - '3.8.2'
      specs:
      - https://anaconda.org/bioconda/rtg-tools

arguments:
- valueFrom: vcfeval
  position: 2
- valueFrom: 20G
  position: 1
  prefix: RTG_MEM=
  separate: false
- valueFrom: "$(runtime.outdir)/out"
  prefix: -o
  position: 3
- valueFrom: $(runtime.cores)
  prefix: -T
  position: 4

inputs:
  rtg_reference:
    type: Directory
    inputBinding:
      position: 5
      prefix: -t
  gold_standard:
    type: File
    inputBinding:
      position: 6
      prefix: -b
    secondaryFiles:
    - .tbi
    doc: Genome-In-A-Bottle gold start VCF.
  input:
    type: File
    inputBinding:
      position: 7
      prefix: -c
    secondaryFiles:
    - .tbi
    doc: input compressed and index VCF
  all_records:
    type: boolean
    inputBinding:
      position: 8
      prefix: --all-records
  sample_names:
    type: string
    inputBinding:
      prefix: --sample=
      separate: false
      position: 9
  evaluation_regions:
    type: File
    inputBinding:
      prefix: --evaluation-regions=
      separate: false
      position: 10

outputs:
  output:
    type: Directory
    outputBinding:
      glob: "$(runtime.outdir)/out"

Answer 1

[Michael R. Crusoe]

Hello h.mon,

When I've had this issue in the past I've fixed it by running cwltool inside a Python 2.7 virtualenv. But this is a bug, so I've opened an issue at https://github.com/common-workflow-language/cwltool/issues/954 to track it.

Thanks!

Answer 2

[sf21]

Thanks for replying and opening a ticket. This is working in cwltool version 1.0.20181012180214 and Python version 3.5.5. In Python 2.7, i am able to run using conda (--beta-conda-dependencies) but not using modules (--beta-dependency-resolvers-configuration).