diff wine_quality.xml @ 2:c1b75945752a draft

planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality commit c595a7b4b556ab642ecf0396957f2959139dc4ab-dirty
author siwaa
date Mon, 09 Dec 2024 10:31:09 +0000
parents c3841488b88d
children f542f29a920c
line wrap: on
line diff
--- a/wine_quality.xml	Wed Dec 04 18:35:18 2024 +0000
+++ b/wine_quality.xml	Mon Dec 09 10:31:09 2024 +0000
@@ -5,23 +5,20 @@
   <requirements>
 
     <!-- singularity -->
-    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/dnn_fidlemore:6d159f79349e231deadb738f79bd293c1a8dadd3</container>
+    <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/use/dnn_fidlemore:c595a7b4b556ab642ecf0396957f2959139dc4ab</container>
 
     <!-- image locale
     <container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/USE_branch_dnn/use/DNN/containers/fidlemore.simg</container -->
 
   </requirements>
 
-  <environment_variables>
-    <environment_variable name="FIDLE_DATASETS_DIR">/fidle-tp/datasets-fidle</environment_variable>
-  </environment_variables>
   <command detect_errors="aggressive">
     <![CDATA[
-    . /fidle-tp/fidle-env/bin/activate;
-    mkdir /fidle-tp/fidle-env/cache_dir; export TRANSFORMERS_CACHE=/fidle-tp/fidle-env/cache_dir;
-    mkdir /fidle-tp/fidle-env/mpl_dir; export MPLCONFIGDIR=/fidle-tp/fidle-env/mpl_dir;
-    /bin/bash -c "python3 $__tool_directory__/wine_quality.py -model_ckpt_filepath ${model_ckpt} -norm_config_json_filepath ${norm_config_json} -data '${datajson_text}'";
-    cp OUTPUTS/quality.txt ${quality_txt};
+    bash -e -c "source /fidle-tp/fidle-env/bin/activate &&
+    mkdir datasets-fidle &&
+    export FIDLE_DATASETS_DIR=\$(realpath -s datasets-fidle) &&
+    python3 $__tool_directory__/wine_quality.py -model_ckpt_filepath ${model_ckpt} -norm_config_json_filepath ${norm_config_json} -data '${datajson_text}' &&
+    cp OUTPUTS/quality.txt ${quality_txt}"
     ]]>
   </command>