Mercurial > repos > bgruening > package_rdkit_2013_03

changeset 2:c62dbe7147ad

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Uploaded
author bgruening
date Sat, 11 May 2013 16:08:00 -0400
parents 0275ed826890
children 77b168565931
files tool_dependencies.xml
diffstat 1 files changed, 43 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Sat Apr 27 13:21:08 2013 -0400
+++ b/tool_dependencies.xml	Sat May 11 16:08:00 2013 -0400
@@ -1,5 +1,46 @@
 <tool_dependency>
-    <package name="rdkit" version="2012_12_1">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_rdkit_2013_03" owner="bgruening" changeset_revision="c7f8a12d8176" prior_installation_required="True" />
+    <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="boost" version="1.53.0">
+        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_boost_1_53" owner="bgruening" changeset_revision="f4209b50c801" prior_installation_required="True" />
+    </package>
+
+    <package name="rdkit" version="2013_03_2">
+        <install version="1.0">
+            <actions>
+                <!-- first action is always downloading -->
+                <action type="download_by_url">http://rdkit.googlecode.com/files/RDKit_2013_03_2.tgz</action>
+
+                <!-- populate the environment variables from the dependend repos -->
+                <action type="set_environment_for_install">
+                    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="bgruening" changeset_revision="c3041382815c">
+                        <package name="numpy" version="1.7.1" />
+                    </repository>
+                </action>
+                <action type="set_environment_for_install">
+                    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_boost_1_53" owner="bgruening" changeset_revision="f4209b50c801">
+                        <package name="boost" version="1.53.0" />
+                    </repository>
+                </action>
+
+                <!-- PYTHONPATH_NUMPY is set in the numpy package -->
+                <action type="shell_command">export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`pwd`/lib/ &amp;&amp;
+                    export PYTHONPATH=$PYTHONPATH:`pwd`/ &amp;&amp;
+                    mkdir build &amp;&amp;
+                    cd build &amp;&amp;
+                    cmake .. -DBOOST_ROOT=$BOOST_ROOT_DIR -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/rdkit/ -DRDK_INSTALL_INTREE=OFF -DPYTHON_NUMPY_INCLUDE_PATH=$PYTHONPATH_NUMPY/numpy/core/include/</action>
+                <action type="shell_command">cd ./build &amp;&amp; make </action>
+                <action type="shell_command">cd ./build &amp;&amp; make install</action>
+
+                <action type="set_environment">
+                    <environment_variable name="RDBASE" action="set_to">$INSTALL_DIR/rdkit</environment_variable>
+                    <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/rdkit</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/rdkit/bin</environment_variable>
+                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/rdkit/lib</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling rdkit requires cmake, python headers, sqlite3, flex and bison.</readme>
     </package>
 </tool_dependency>