diff --git a/Dockerfile b/Dockerfile index 10a1156..8dd6572 100644 --- a/Dockerfile +++ b/Dockerfile @@ -96,8 +96,9 @@ RUN cd $tmp_install_dir && \ #RUN source activate $MINICONDA_PREFIX/bin/conda && \ # conda activate daops && \ -RUN $MINICONDA_PREFIX/envs/daops/bin/pip uninstall roocs_utils -y && \ - $MINICONDA_PREFIX/envs/daops/bin/pip install roocs-utils@git+https://github.com/roocs/roocs-utils.git@i106-enable-read-kerchunk#egg=roocs_utils +RUN $MINICONDA_PREFIX/envs/daops/bin/pip uninstall roocs_utils -y && \ + $MINICONDA_PREFIX/envs/daops/bin/pip install \ + roocs-utils@git+https://github.com/roocs/roocs-utils.git@master#egg=roocs_utils # ==== Create a directory that we can bind-mount ==== RUN mkdir /outputs @@ -110,7 +111,7 @@ RUN rm -fr /var/lib/{apt,dpkg,cache,log} #COPY ./kc-script.py /tmp/kc-script.py #RUN $MINICONDA_PREFIX/envs/daops/bin/python /tmp/kc-script.py -# ==== Run daops at the command-line ==== +# ==== Test run daops at the command-line ==== RUN ROOCS_CONFIG=$config_file $MINICONDA_PREFIX/envs/daops/bin/daops subset --area 0,-10,120,40 \ --time 2085-01-16/2120-12-16 --levels / --time-components year:2090,2091,2092 \ --output-dir /tmp --file-namer simple cmip5.output1.MOHC.HadGEM2-ES.rcp85.mon.atmos.Amon.r1i1p1.latest.tas diff --git a/app-package.cwl b/app-package.cwl index 38669cf..8780da7 100644 --- a/app-package.cwl +++ b/app-package.cwl @@ -15,9 +15,18 @@ $graph: - class: ScatterFeatureRequirement inputs: + area: + doc: area + type: string time: doc: time type: string + time_components: + doc: time_components + type: string + levels: + doc: levels + type: string collection: doc: collection type: string @@ -38,7 +47,10 @@ $graph: subset: run: "#clt" in: + area: area time: time + time_components: time_components + levels: levels collection: collection file_namer: file_namer output_dir: output_dir @@ -53,8 +65,6 @@ $graph: envDef: ROOCS_CONFIG: /root/roocs.ini # PATH: /srv/conda/envs/env_crop/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin -# PYTHONPATH: /home/jovyan/ogc-eo-application-package-hands-on/water-bodies/command-line-tools/crop:/home/jovyan/water-bodies/command-line-tools/crop:/workspaces/vscode-binder/command-line-tools/crop -# PROJ_LIB: /srv/conda/envs/env_crop/share/proj/ # ResourceRequirement: # coresMax: 1 # ramMax: 500Mb @@ -65,25 +75,40 @@ $graph: arguments: [] inputs: + area: + type: string + inputBinding: + prefix: --area + position: 1 time: type: string inputBinding: prefix: --time - position: 1 + position: 2 + time_components: + type: string + inputBinding: + prefix: --time-components + position: 3 + levels: + type: string + inputBinding: + prefix: --levels + position: 4 file_namer: type: string inputBinding: prefix: --file-namer - position: 2 + position: 5 output_dir: type: string inputBinding: prefix: --output-dir - position: 3 + position: 6 collection: type: string inputBinding: - position: 4 + position: 7 outputs: results: outputBinding: