Mercurial > repos > bgruening > osra

changeset 2:abe9670bfc44

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Uploaded
author bgruening
date Fri, 12 Apr 2013 16:25:32 -0400
parents 4a71d98176f6
children deccc074dbfb
files osra.xml tool_dependencies.xml
diffstat 2 files changed, 10 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/osra.xml	Sun Mar 31 13:12:44 2013 -0400
+++ b/osra.xml	Fri Apr 12 16:25:32 2013 -0400
@@ -4,7 +4,14 @@
         <requirement type="package" version="1.4.0">osra</requirement>
     </requirements>
     <command>
-        osra -f $oformat $infile > $outfile
+        ## OSRA_DATA_FILES is set during the toolshed Installation
+        ## if it is not set, use the standard configuration and hope the best
+        osra -f $oformat $infile 
+        #import os
+        #if os.environ.get('OSRA_DATA_FILES', None):
+            -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt
+        #end if
+        > $outfile
     </command>
     <inputs>
         <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/>
--- a/tool_dependencies.xml	Sun Mar 31 13:12:44 2013 -0400
+++ b/tool_dependencies.xml	Fri Apr 12 16:25:32 2013 -0400
@@ -49,12 +49,10 @@
 
                 <action type="set_environment">
                     <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/gmagick/build/lib/</environment_variable>
-                </action>
-                <action type="set_environment">
                     <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/potrace/build/lib/</environment_variable>
-                </action>
-                <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <!-- OSRA_DATA_FILES is only used by the galaxy wrapper and is not part of OSRA -->
+                    <environment_variable name="OSRA_DATA_FILES" action="prepend_to">$INSTALL_DIR/share</environment_variable>
                 </action>
             </actions>
         </install>