| Next changeset 1:b93c068b0920 (2015-07-17) |
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Commit message:
Uploaded |
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added:
tool_dependencies.xml |
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| diff -r 000000000000 -r f2676c09c535 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Aug 15 03:14:20 2013 -0400 |
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| @@ -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 && + 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> |