Commit e7bd4add authored by Ronan Trepos's avatar Ronan Trepos
Browse files

test galaxy tool

parent 8526319d
......@@ -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>"
......@@ -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
......
categories: [AgroEcosystems]
description: Azodyn simulations tool
name: razodyn
owner: siwaa
<?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>
......@@ -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>
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