Mercurial > repos > iuc > package_chemfp_1_1

changeset 0:f2676c09c535 draft

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Uploaded
author bgruening
date Thu, 15 Aug 2013 03:14:20 -0400
parents
children b93c068b0920
files tool_dependencies.xml
diffstat 1 files changed, 34 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Aug 15 03:14:20 2013 -0400
@@ -0,0 +1,34 @@
+<tool_dependency>
+    <package name="chemfp" version="1.1p1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://chem-fingerprints.googlecode.com/files/chemfp-1.1p1.tar.gz</action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
+                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
+                </action>
+
+                <!-- apply one small patched file, to support the query-format target-format commandline options 
+                <action type="download_file">http://chem-fingerprints.googlecode.com/hg-history/1281bfcb470b84f5e75250dfa041345d280dde30/chemfp/commandline/simsearch.py</action>-->
+                <action type="download_file">http://share.gruenings.eu/simsearch.py</action>
+                <action type="shell_command">rm $INSTALL_DIR/lib/python/chemfp/commandline/simsearch.py</action>
+                <action type="move_file">
+                    <source>simsearch.py</source>
+                    <destination>$INSTALL_DIR/lib/python/chemfp/commandline/</destination>
+                </action>
+                <!-- end patching -->
+
+                <action type="set_environment">
+                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+        The core chemfp functionality does not depend on a third-party library but you will need a chemistry toolkit in order to generate new fingerprints 
+        from structure files. chemfp supports the free Open Babel and RDKit toolkits and the proprietary OEChem toolkit.
+        Currently the Galaxy-wrappers are using openbabel and rdkit as underlying toolkit.
+        Compiling chemfp requires gcc and a python2.5+ version.</readme>
+    </package>
+</tool_dependency>