Mercurial > repos > bgruening > silicos_it
changeset 1:54edf22c93c0
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 26 Apr 2013 08:05:46 -0400 |
| parents | 80efb29755f3 |
| children | 4ac14b5bacf1 |
| files | qed/silicos_qed.xml tool_dependencies.xml |
| diffstat | 2 files changed, 26 insertions(+), 37 deletions(-) [+] |
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--- 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>
--- 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 && make && 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 $OPENBABEL_LIB_DIR + --> + <action type="set_environment_for_install"> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="6fd6b904eeff"> + <package name="openbabel" version="2.3.2" /> + </repository> + </action> <!--compiling strip-it --> - <action type="shell_command">wget http://www.silicos-it.com/_php/download.php?file=strip-it-1.0.1.tar.gz</action> - <action type="shell_command">tar xfvz download.php?file=strip-it-1.0.1.tar.gz && - cd strip-it-1.0.1 && - cmake . -DOPENBABEL2_INCLUDE_DIRS=$INSTALL_DIR/openbabel/build/include/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/strip-it/ -DOPENBABEL2_LIBRARIES=$INSTALL_DIR/openbabel/build/lib/libopenbabel.so && + <action type="shell_command"> + cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/strip-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so && make && make install</action> <action type="set_environment"> @@ -21,7 +36,7 @@ <action type="shell_command">wget http://www.silicos-it.com/_php/download.php?file=align-it-1.0.3.tar.gz</action> <action type="shell_command">tar xfvz download.php?file=align-it-1.0.3.tar.gz && cd align-it-1.0.3 && - cmake . -DOPENBABEL2_INCLUDE_DIRS=$INSTALL_DIR/openbabel/build/include/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/align-it/ -DOPENBABEL2_LIBRARIES=$INSTALL_DIR/openbabel/build/lib/libopenbabel.so && + cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/align-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so && make && make install</action> <action type="set_environment"> @@ -32,41 +47,15 @@ <action type="shell_command">wget http://www.silicos-it.com/_php/download.php?file=shape-it-1.0.1.tar.gz</action> <action type="shell_command">tar xfvz download.php?file=shape-it-1.0.1.tar.gz && cd shape-it-1.0.1 && - cmake . -DOPENBABEL2_INCLUDE_DIRS=$INSTALL_DIR/openbabel/build/include/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/shape-it/ -DOPENBABEL2_LIBRARIES=$INSTALL_DIR/openbabel/build/lib/libopenbabel.so && + cmake . -DOPENBABEL2_INCLUDE_DIRS=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/shape-it/ -DOPENBABEL2_LIBRARIES=$OPENBABEL_LIB_DIR/libopenbabel.so && make && make install</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$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 && - cd boost_1_53_0 && - ./bootstrap.sh --with-libraries=python,regex && - 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/ && - export PYTHONPATH=$PYTHONPATH:`pwd`/ && - cd RDKit_2012_12_1 && - mkdir build && - cd build && - cmake .. -DBOOST_ROOT=$INSTALL_DIR/boost/ -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/rdkit/ -DRDK_INSTALL_INTREE=OFF</action> - <action type="shell_command">cd RDKit_2012_12_1/build && make </action> - <action type="shell_command">cd RDKit_2012_12_1/build && make install</action> - - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$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>