diff wine_quality_predict.xml @ 2:4d31508e95c6 draft

planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/use/-/tree/dnn/DNN/galaxy-tools/wine_quality_predict commit 58f66f614dc32b7550ac23e52d84248ddc802863-dirty
author siwaa
date Fri, 06 Dec 2024 19:17:19 +0000
parents f9637dc4e18a
children 01bf4f689614
line wrap: on
line diff
--- a/wine_quality_predict.xml	Wed Dec 04 18:35:11 2024 +0000
+++ b/wine_quality_predict.xml	Fri Dec 06 19:17:19 2024 +0000
@@ -17,11 +17,19 @@
   </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 /fidlemore/model_wine_lightning/wine_quality_predict.py -model_ckpt_filepath ${model_ckpt} -norm_config_json_filepath ${norm_config_json} -data_json_filepath ${data_json}";
-    cp OUTPUTS/report.json ${report_json};
+
+    bash -e -c "source /fidle-tp/fidle-env/bin/activate &&
+    mkdir datasets-fidle &&
+    export FIDLE_DATASETS_DIR=\$(realpath -s datasets-fidle) &&
+    mkdir ipython_dir &&
+    export IPYTHONDIR=\$(realpath -s ipython_dir) &&
+    ipython profile create default &&
+    mkdir cache_dir &&
+    export TRANSFORMERS_CACHE=\$(realpath -s cache_dir) &&
+    mkdir mpl_dir &&
+    export MPLCONFIGDIR=\$(realpath -s mpl_dir) &&
+    python3 /fidlemore/model_wine_lightning/wine_quality_predict.py -model_ckpt_filepath ${model_ckpt} -norm_config_json_filepath ${norm_config_json} -data_json_filepath ${data_json} &&
+    cp OUTPUTS/report.json ${report_json}"
     ]]>
   </command>