fIx read only julia depot

ogc-app-cwl/Dockerfile

@@ -1,12 +1,14 @@
 FROM julia:1.11.2-bookworm
 WORKDIR /work
 
-ENV JULIA_PROJECT=/work
 ENV JULIA_NUM_THREADS=auto
 
-COPY Project.toml .
-COPY Manifest.toml .
-RUN julia -e 'using Pkg; Pkg.instantiate()'
+ENV JULIA_DEPOT_PATH=/.julia
+RUN julia -e 'using Pkg; Pkg.activate("/.julia/environments/v1.11"); Pkg.instantiate(); Pkg.status()'
+COPY Project.toml /.julia/environments/v1.11/
+COPY Manifest.toml /.julia/environments/v1.11/
+RUN julia -e 'using Pkg; Pkg.activate("/.julia/environments/v1.11"); Pkg.instantiate(); Pkg.status()'
+ENV JULIA_DEPOT_PATH=~/.julia:/.julia
 
 ADD run.jl ./
-ENTRYPOINT ["/work/run.jl"]
+ENTRYPOINT ["/work/run.jl"]

ogc-app-cwl/fairsendd.cwl

@@ -18,7 +18,7 @@ $graph:
   outputs:
     out_cube:
       doc: Path to output zarr data cube
-      type: string
+      type: File
       outputSource: rqa/out_cube
 
   steps:
@@ -49,12 +49,7 @@ $graph:
 
   outputs:
     out_cube:
-      type: string
-      outputBinding:
-        glob: stdout.txt
-        outputEval: self[0].contents
-        loadContents: true
-  stdout: stdout.txt
+      type: stdout
   id: cmd-rqa
 $namespaces:
   edam: http://edamontology.org/

ogc-app-cwl/run.jl

@@ -1,7 +1,8 @@
-#!/usr/bin/env -S julia --color=yes --startup-file=no --project=. --threads=auto
+#!/usr/bin/env -S julia --color=yes --startup-file=no --threads=auto
 
-using YAXArrays: YAXDefaults
+using Pkg
 using Glob: glob
+using YAXArrays: YAXDefaults
 using ArgParse
 using RQADeforestation: gdalcube, rqatrend
 using DimensionalData: (..)

ogc-app-cwl/run.sh

@@ -1,5 +1,8 @@
 #! /usr/bin/env sh
 
-docker build . -t danlooo/cwl-example
-docker push danlooo/cwl-example
-cwltool example.cwl#add-numbers -a 1.2 -b 3.4
+docker build . -t danlooo/fairsendd
+docker push danlooo/fairsendd
+
+cwltool fairsendd.cwl#rqa --continent AF --tile E036N075T3
+docker run danlooo/fairsendd AF E036N075T3
+docker run --env=HOME=/tmp/YgEokx --user 1234:1234 danlooo/fairsendd AF E036N075T3