Mercurial > repos > kkonganti > lexmapr2_from_cfsan

diff cfsan_lexmapr2.xml @ 13:bdccef316f65

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"planemo upload"
author kkonganti
date Thu, 15 Sep 2022 14:11:09 -0400
parents 530cafac56f9
children 89998b9b4d46
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--- a/cfsan_lexmapr2.xml	Thu Sep 15 13:55:38 2022 -0400
+++ b/cfsan_lexmapr2.xml	Thu Sep 15 14:11:09 2022 -0400
@@ -13,8 +13,8 @@
     </requirements>
     <version_command>python $__tool_directory__/lexmapr2.py --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-    echo \$PYTHONPATH 1>&2;
     mkdir -p lexmapr2-input || exit 1;
+    ln -sf '/tool/tool-data/cfsan_lexmapr2/0/lexmapr' .;
     ln -sf '$input' './lexmapr2-input/$input.name';
     python $__tool_directory__/lexmapr2.py
     #if ($embl_ont != ""):
@@ -39,7 +39,6 @@
     ]]></command>
     <environment_variables>
         <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
-        <environment_variable name="PYTHONPATH">/tool/tool-data/cfsan_lexmapr2/0</environment_variable>
     </environment_variables>
     <inputs>
         <param name="input" type="data" format="csv" label="Input CSV"