Mercurial > repos > yating-l > jbrowsearchivecreator

diff tool_dependencies.xml @ 19:62dee5369e80 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit afd782e8741a859506794bea92475f620265c50e
author sargentl
date Thu, 13 Sep 2018 17:43:23 -0400
parents 7cb67cbbd8e5
children
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--- a/tool_dependencies.xml	Fri Jul 20 12:25:36 2018 -0400
+++ b/tool_dependencies.xml	Thu Sep 13 17:43:23 2018 -0400
@@ -18,7 +18,7 @@
 
     <package name="biopython" version="1.68">
         <readme>
-This package is based on package_biopython_1_67 owned by biopython. 
+This package is based on package_biopython_1_67 owned by biopython.
 https://toolshed.g2.bx.psu.edu/repository?user_id=fd5c6d0f82f315d8
 
 This Galaxy Tool Shed package installs Biopython from source, having
@@ -41,10 +41,10 @@
                 </action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
-                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
-                    export PATH=$PATH:$PATH_NUMPY &amp;&amp; 
-                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp; 
-                    python setup.py install --install-lib $INSTALL_DIR/lib/python
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
+                    export PATH=$PATH:$PATH_NUMPY &amp;&amp;
+                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
+                    python2 setup.py install --install-lib $INSTALL_DIR/lib/python
                 </action>
                 <action type="set_environment">
                     <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
@@ -66,9 +66,9 @@
                         export HOME=$INSTALL_DIR/jbrowse &amp;&amp; ./setup.sh
                     </action>
                     <action type="move_directory_files">
-                        <source_directory>.</source_directory>                       
+                        <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR/jbrowse</destination_directory>
-                    </action>    
+                    </action>
                     <action type="set_environment">
                         <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse</environment_variable>
                         <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/bin</environment_variable>