Commit 1d7f61a0 authored by Tammo Jan Dijkema's avatar Tammo Jan Dijkema

Add H5ParmCollector

parent 33498fbe
Pipeline #172 passed with stages
in 8 minutes and 22 seconds
......@@ -64,6 +64,12 @@ NDPPP:
script:
- cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH steps/DPPP.cwl test_jobs/NDPPP.json
h5parm_collector:
stage: test_steps
allow_failure: true
script:
- cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/H5ParmCollector.cwl test_jobs/h5parm_collector.json
aoflagger:
stage: test_steps
allow_failure: true
......@@ -82,6 +88,12 @@ interpolate_visibilities:
script:
- cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/interpolate_visibilities.cwl test_jobs/interpolate_visibilities.json
h5parm_collector:
stage: test_steps
allow_failure: true
script:
- cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/H5ParmCollector.cwl test_jobs/h5parm_collector.json
blsmooth:
stage: test_steps
allow_failure: true
......
......@@ -93,8 +93,11 @@ ARG LSMTool_TAG=master
RUN apt-get update && apt-get install -y nodejs python3-pip git wsclean
RUN python3 -m pip install cwltool cwl-runner -e "git://github.com/darafferty/LSMTool.git@${LSMTool_TAG}#egg=LSMTool"
RUN python3 -m pip install git+https://github.com/revoltek/losoto.git
ADD L570745_uv_first10.MS.tar.xz /data
ADD skymodels.tar.gz /data/skymodels
ADD example.h5 /data
ADD .entrypoint /home/lofaruser/.entrypoint
RUN chown lofaruser:lofaruser /home/lofaruser/.entrypoint && \
chmod +rx /home/lofaruser/.entrypoint
......
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.0
id: h5parm_collector
hints:
DockerRequirement:
dockerPull: tammojan/lofar-pipeline
baseCommand:
- H5parm_collector.py
inputs:
- id: h5parmFiles
type: File[]
doc: List of h5parm files
inputBinding:
position: 0
- id: insolset
type: string?
default: sol000
doc: Input solset name
inputBinding:
prefix: --insolset
- id: outh5parmname
type: string
doc: Output h5parm name
default: output.h5
outputs:
- id: outh5parm
doc: Output h5parm
type: File
outputBinding:
glob: $(inputs.outh5parmname)
label: H5parm_collector
{
"h5parmFiles": [
{
"class": "File",
"path": "/data/example.h5"
}
]
}
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