test galaxy tool

siwaa_recipe/README.txt

@@ -29,7 +29,20 @@ docker run -v $PWD:/work rtrepos/azodyn_test /bin/bash -c "Rscript --verbose /da
 cp ../AZODYN/data/Breteniere_1991_2018.csv Breteniere_1991_2018_test.csv
 singularity exec --cleanenv -B $PWD:/work docker://rtrepos/azodyn_test:latest /bin/bash -c "Rscript --verbose /data/azodyn/siwaa_recipe/razodyn.R /work/file_input.csv /work/file_outputs.csv > /work/razodyn.txt"
 
+# with singularity without mounted PWD
 
 singularity exec docker://rtrepos/azodyn_test:latest /bin/bash -c "Rscript --verbose /data/azodyn/siwaa_recipe/razodyn.R file_input.csv file_outputs.csv 3"
 
 
+####planemo
+
+cd galaxy_tools ;
+planemo serve --job_config_file ./job_conf.xml tools_AZODYN.xml
+
+## publish on toolshed
+
+planemo shed_create --shed_target "http://147.100.179.176:9009/" --shed_email "siwaa@inra.fr" --shed_password "<TODO>"
+
+
+
+

siwaa_recipe/container/Dockerfile

@@ -52,7 +52,7 @@ RUN cd RECORD/pkgs \
     && vle -P vle.discrete-time.generic clean rclean configure build
 
 RUN git clone https://forgemia.inra.fr/record/azodyn.git \
-    &&    cd azodyn \
+    && cd azodyn \
     && git checkout origin/siwaa -b siwaa \
     && vle -P AZODYN configure build
 

siwaa_recipe/galaxy_tools/.shed.yml

+categories: [AgroEcosystems]
+description: Azodyn simulations tool
+name: razodyn
+owner: siwaa

siwaa_recipe/galaxy_tools/job_conf.xml

+<?xml version="1.0"?>
+<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
+<job_conf>
+    <plugins>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
+    </plugins>
+    <destinations>
+      <destination id="local" runner="local">
+	<param id="singularity_enabled">true</param>
+      </destination>
+    </destinations>
+</job_conf>

siwaa_recipe/galaxy_tools/tools_AZODYN.xml

@@ -4,20 +4,21 @@
     <container type="singularity">docker://rtrepos/azodyn_test:latest</container>
   </requirements>
   <command detect_errors="aggressive">
-    cp ${input_meteo} /data/pkgs-2.0/AZODYN/data/; 
-    Rscript --verbose razodyn.R ${file_input} ${file_outputs} > ${razodyn_log}";
-    zip ${razodyn_results} razodyn_results_*;
+    unzip ${input_meteo}; 
+    /bin/bash -c "Rscript --verbose /data/azodyn/siwaa_recipe/razodyn.R ${file_input} ${file_outputs} 3";
+    zip temp_results.zip  razodyn_results_*.txt;
+    cp temp_results.zip ${razodyn_results};
   </command>
   <inputs>
-    <param name="input_meteo" type="data" format="csv" label="input meteo"/>
+    <param name="input_meteo" type="data" format="zip" label="input meteo (zip file)"/>
     <param name="file_input" type="data" format="csv" label="azodyn inputs"/>
     <param name="file_outputs" type="data" format="csv" label="azodyn outputs"/>
   </inputs>
   <outputs>
     <data format="zip" name="razodyn_results" />
-    <data format="txt" name="razodyn_log" />
   </outputs>
   <help>
 razodyn help
   </help>
 </tool>
+