# HG changeset patch
# User bgruening
# Date 1366977946 14400
# Node ID 54edf22c93c0acfe2b1de56f6b5681d325b20190
# Parent  80efb29755f3f195044622b4f86f8686d2aefcc3
Uploaded

diff -r 80efb29755f3 -r 54edf22c93c0 qed/silicos_qed.xml
--- a/qed/silicos_qed.xml	Sun Mar 31 13:16:06 2013 -0400
+++ b/qed/silicos_qed.xml	Fri Apr 26 08:05:46 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="silicos_qed" name="Drug-likeness">
+<tool id="silicos_qed" name="Drug-likeness" version="0.1">
   <description>quantitative estimation (QED)</description>
   <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
   <requirements>
diff -r 80efb29755f3 -r 54edf22c93c0 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Mar 31 13:16:06 2013 -0400
+++ b/tool_dependencies.xml	Fri Apr 26 08:05:46 2013 -0400
@@ -1,16 +1,31 @@
 <tool_dependency>
+    <package name="numpy" version="1.7.1">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="bgruening" changeset_revision="c3041382815c" prior_installation_required="True" />
+    </package>
+    <package name="openbabel" version="2.3.2">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="6fd6b904eeff" prior_installation_required="True" />
+    </package>
+    <package name="rdkit" version="2012_12_1">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_rdkit_2012_12" owner="bgruening" changeset_revision="0adc830e7d71" />
+    </package>
     <package name="silicos_it" version="1.0.0">
         <install version="1.0">
             <actions>
-                <!--compiling openbabel 2.3.2 -->
-                <action type="download_by_url">http://downloads.sourceforge.net/project/openbabel/openbabel/2.3.2/openbabel-2.3.2.tar.gz</action>
-                <action type="shell_command">cmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/openbabel/build &amp;&amp; make &amp;&amp; make install</action>
+                <!-- 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 toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="6fd6b904eeff">
+                        <package name="openbabel" version="2.3.2" />
+                    </repository>
+                </action>
 
                 <!--compiling strip-it -->
-                <action type="shell_command">wget http://www.silicos-it.com/_php/download.php?file=strip-it-1.0.1.tar.gz</action>
-                <action type="shell_command">tar xfvz download.php?file=strip-it-1.0.1.tar.gz &amp;&amp; 
-                    cd strip-it-1.0.1 &amp;&amp;
-                    cmake . -DOPENBABEL2_INCLUDE_DIRS=$INSTALL_DIR/openbabel/build/include/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/strip-it/ -DOPENBABEL2_LIBRARIES=$INSTALL_DIR/openbabel/build/lib/libopenbabel.so &amp;&amp; 
+                <action type="shell_command">
+                    cmake . -DOPENBABEL2_INCLUDE_DIRS=$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">
@@ -21,7 +36,7 @@
                 <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; 
-                    cmake . -DOPENBABEL2_INCLUDE_DIRS=$INSTALL_DIR/openbabel/build/include/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/align-it/ -DOPENBABEL2_LIBRARIES=$INSTALL_DIR/openbabel/build/lib/libopenbabel.so &amp;&amp; 
+                    cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/align-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so &amp;&amp; 
                     make &amp;&amp; 
                     make install</action>
                 <action type="set_environment">
@@ -32,41 +47,15 @@
                 <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; 
-                    cmake . -DOPENBABEL2_INCLUDE_DIRS=$INSTALL_DIR/openbabel/build/include/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/shape-it/ -DOPENBABEL2_LIBRARIES=$INSTALL_DIR/openbabel/build/lib/libopenbabel.so &amp;&amp; 
+                    cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/shape-it/ -DOPENBABEL2_LIBRARIES=$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/shape-it/bin</environment_variable>
                 </action>
 
-                <!-- RDKit with boost, required for QED -->
-                <!-- try to set the right architecture with uname -m -->
-                <action type="shell_command">wget http://downloads.sourceforge.net/project/boost/boost/1.53.0/boost_1_53_0.tar.bz2</action>
-                <action type="shell_command">tar xfvj boost_1_53_0.tar.bz2 &amp;&amp; 
-                    cd boost_1_53_0 &amp;&amp;
-                    ./bootstrap.sh --with-libraries=python,regex &amp;&amp; 
-                    if [ $(uname -m) == 'x86_64' ]; then ./bjam install --prefix=$INSTALL_DIR/boost/; else ./bjam address-model=64 cflags=-fPIC cxxflags=-fPIC install --prefix=$INSTALL_DIR/boost/; fi;</action>
-                <!-- QED -->
-                <action type="shell_command">wget http://downloads.sourceforge.net/project/rdkit/rdkit/Q4_2012/RDKit_2012_12_1.tgz</action>
-                <action type="shell_command">tar xfvz RDKit_2012_12_1.tgz</action>
-
-                <action type="shell_command">export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`pwd`/RDKit_2012_12_1/lib/ &amp;&amp;
-                    export PYTHONPATH=$PYTHONPATH:`pwd`/ &amp;&amp;
-                    cd RDKit_2012_12_1 &amp;&amp;
-                    mkdir build &amp;&amp;
-                    cd build &amp;&amp;
-                    cmake .. -DBOOST_ROOT=$INSTALL_DIR/boost/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/rdkit/ -DRDK_INSTALL_INTREE=OFF</action>
-                    <action type="shell_command">cd RDKit_2012_12_1/build &amp;&amp; make </action>
-                    <action type="shell_command">cd RDKit_2012_12_1/build &amp;&amp; make install</action>
-
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/rdkit/bin</environment_variable>
-                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/rdkit/lib/</environment_variable>
-                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/boost/lib/</environment_variable>
-                </action>
-
             </actions>
         </install>
-        <readme>Compiling OpenBabel requires g++ and CMake 2.4+. Optional but required for a few features is Eigen version 2 or newer and the cairo development libraries.</readme>
+        <readme>Compiling silicos-it requires g++ and CMake 2.4+.</readme>
     </package>
 </tool_dependency>