# HG changeset patch
# User Bjoern Gruening <bjoern.gruening@gmail.com>
# Date 1369658077 -7200
# Node ID c904022ce8e2c2da9d1de14f2e1c8860fa0b5ccb
# Parent  c5a538ec7b431f767a45cf536199087c540447ec
updates to silicos-it

diff -r c5a538ec7b43 -r c904022ce8e2 repository_dependencies.xml
--- a/repository_dependencies.xml	Sun May 26 16:50:31 2013 +0200
+++ b/repository_dependencies.xml	Mon May 27 14:34:37 2013 +0200
@@ -1,4 +1,3 @@
-<?xml version="1.0"?>
 <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
-    <repository name="molecule_datatypes" owner="bgruening" />
-</repositories> 
+    <repository changeset_revision="c5383bd4d006" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+</repositories>
diff -r c5a538ec7b43 -r c904022ce8e2 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun May 26 16:50:31 2013 +0200
+++ b/tool_dependencies.xml	Mon May 27 14:34:37 2013 +0200
@@ -1,39 +1,37 @@
 <tool_dependency>
     <package name="numpy" version="1.7.1">
-        <repository name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" />
+        <repository changeset_revision="1aa6410e151b" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="openbabel" version="2.3.2">
-        <repository name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" />
+        <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="rdkit" version="2012_12_1">
-        <repository name="package_rdkit_2012_12" owner="bgruening" prior_installation_required="True" />
+        <repository changeset_revision="884c95a27e40" name="package_rdkit_2012_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
     <package name="silicos_it" version="1.0.0">
         <install version="1.0">
             <actions>
-                <!-- first action is always downloading -->
+                
                 <action type="download_by_url">http://www.silicos-it.com/_php/download.php?file=strip-it-1.0.1.tar.gz</action>
 
-                <!-- populate the environment variables from the dependend repos 
-                    $OPENBABEL_INCLUDE_DIR and $OPENBABEL_LIB_DIR
-                -->
+                
                 <action type="set_environment_for_install">
-                    <repository name="package_openbabel_2_3" owner="bgruening">
+                    <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                         <package name="openbabel" version="2.3.2" />
                     </repository>
                 </action>
 
-                <!--compiling strip-it -->
+                
                 <action type="shell_command">
                     cd strip-it-1.0.1 &amp;&amp;
                     cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/strip-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so &amp;&amp; 
                     make  &amp;&amp;
                     make install</action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/strip-it/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/strip-it/bin</environment_variable>
                 </action>
 
-                <!-- compiling align-it -->
+                
                 <action type="shell_command">wget http://www.silicos-it.com/_php/download.php?file=align-it-1.0.3.tar.gz</action>
                 <action type="shell_command">tar xfvz download.php?file=align-it-1.0.3.tar.gz &amp;&amp; 
                     cd align-it-1.0.3 &amp;&amp; 
@@ -41,10 +39,10 @@
                     make &amp;&amp; 
                     make install</action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/align-it/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/align-it/bin</environment_variable>
                 </action>
 
-                <!-- compiling shape-it -->
+                
                 <action type="shell_command">wget http://www.silicos-it.com/_php/download.php?file=shape-it-1.0.1.tar.gz</action>
                 <action type="shell_command">tar xfvz download.php?file=shape-it-1.0.1.tar.gz &amp;&amp; 
                     cd shape-it-1.0.1 &amp;&amp; 
@@ -52,7 +50,7 @@
                     make &amp;&amp; 
                     make install</action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/shape-it/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/shape-it/bin</environment_variable>
                 </action>
 
             </actions>