| Previous changeset 11:143a63ca2bca (2013-05-23) Next changeset 13:ab9e2350406b (2013-05-25) |
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Commit message:
Uploaded |
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modified:
repository_dependencies.xml tool_dependencies.xml |
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added:
tool_dependencies_1_4.xml |
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| diff -r 143a63ca2bca -r f265bcf0ddc5 repository_dependencies.xml --- a/repository_dependencies.xml Thu May 23 16:19:16 2013 -0400 +++ b/repository_dependencies.xml Thu May 23 17:30:05 2013 -0400 |
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| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format)."> - <repository changeset_revision="1b63345907ec" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="bd886859b184" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </repositories> |
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| diff -r 143a63ca2bca -r f265bcf0ddc5 tool_dependencies.xml --- a/tool_dependencies.xml Thu May 23 16:19:16 2013 -0400 +++ b/tool_dependencies.xml Thu May 23 17:30:05 2013 -0400 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="openbabel" version="2.3.2"> - <repository changeset_revision="efffcee80e03" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="graphicsmagick" version="1.3.18"> <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> @@ -14,7 +14,7 @@ <!-- populate the environment variables from the dependend repos --> <action type="set_environment_for_install"> - <repository changeset_revision="efffcee80e03" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu"> <package name="openbabel" version="2.3.2" /> </repository> <repository changeset_revision="34f511310435" name="package_graphicsmagick_1_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu"> |
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| diff -r 143a63ca2bca -r f265bcf0ddc5 tool_dependencies_1_4.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies_1_4.xml Thu May 23 17:30:05 2013 -0400 |
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| @@ -0,0 +1,69 @@ +<tool_dependency> + <package name="openbabel" version="2.3.2"> + <repository name="package_openbabel_2_3" owner="bgruening" prior_installation_required="True" /> + </package> + <package name="graphicsmagick" version="1.3.18"> + <repository name="package_graphicsmagick_1_3" owner="bgruening" prior_installation_required="True" /> + </package> + <package name="osra" version="1.4.0"> + <install version="1.0"> + <actions> + <!-- first action is always downloading --> + <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/1.4.0/osra-1.4.0.tgz</action> + + <!-- populate the environment variables from the dependend repos --> + <action type="set_environment_for_install"> + <repository name="package_openbabel_2_3" owner="bgruening"> + <package name="openbabel" version="2.3.2" /> + </repository> + <repository name="package_graphicsmagick_1_3" owner="bgruening"> + <package name="graphicsmagick" version="1.3.18" /> + </repository> + </action> + + <!--compiling potrace-1.11 --> + <action type="shell_command">wget http://potrace.sourceforge.net/download/potrace-1.11.tar.gz</action> + <action type="shell_command">tar xfvz potrace-1.11.tar.gz && cd potrace-1.11 && ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build && make && make install</action> + + <!--compiling gocr 0.50patched --> + <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action> + <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz && cd gocr-0.50pre-patched && ./configure --prefix=$INSTALL_DIR/gocr/build && make libs && make all install</action> + + <!--compiling tclap 1.2.1 --> + <action type="shell_command">wget http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz</action> + <action type="shell_command">tar xfvz tclap-1.2.1.tar.gz && cd tclap-1.2.1 && ./configure --prefix=$INSTALL_DIR/tclap/build && make && make install</action> + + <!--compiling ocrad 0.21 --> + <action type="shell_command">wget http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action> + <action type="shell_command">tar xfvz ocrad-0.21.tar.gz && cd ocrad-0.21 && ./configure --prefix=$INSTALL_DIR/ocrad/build && make && make install</action> + + <!--compiling cuneiform 1.1.0 --> + <action type="shell_command">wget https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2</action> + <action type="shell_command">tar xfvj cuneiform-linux-1.1.0.tar.bz2 && cd cuneiform-linux-1.1.0 && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ && make && make install</action> + + <!--And finally OSRA 1.4.0--> + <action type="shell_command">wget http://share.gruenings.eu/osra-1.4.0-configure.patch</action> + <action type="shell_command">patch configure < osra-1.4.0-configure.patch</action> + <!-- Extending the PATH is needed for OSRA --> + <action type="shell_command">export PATH=$PATH:$GRAPHICSMAGICK_ROOT_DIR/bin/ && ./configure --with-tclap-include=$INSTALL_DIR/tclap/build/include/ --with-potrace-include=$INSTALL_DIR/potrace/build/include/ --with-potrace-lib=$INSTALL_DIR/potrace/build/lib/ --with-gocr-include=$INSTALL_DIR/gocr/build/include/gocr/ --with-gocr-lib=$INSTALL_DIR/gocr/build/lib/ --with-ocrad-include=$INSTALL_DIR/ocrad/build/include/ --with-ocrad-lib=$INSTALL_DIR/ocrad/build/lib/ --with-cuneiform-include=$INSTALL_DIR/cuneiform/build/install/include/ --with-cuneiform --with-cuneiform-lib=$INSTALL_DIR/cuneiform/build/install/lib/ --with-openbabel-include=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ --with-openbabel-lib=$OPENBABEL_LIB_DIR --with-graphicsmagick-lib=$GRAPHICSMAGICK_ROOT_DIR/lib/ --with-graphicsmagick-include=$GRAPHICSMAGICK_ROOT_DIR/include/GraphicsMagick/ --prefix=$INSTALL_DIR </action> + <action type="shell_command">make</action> + <action type="shell_command">make install</action> + + <action type="shell_command">rm $INSTALL_DIR/tclap/ -r</action> + <!--<action type="shell_command">rm $INSTALL_DIR/openbabel/ -r</action>--> + <action type="shell_command">rm $INSTALL_DIR/gocr/ -r</action> + <action type="shell_command">rm $INSTALL_DIR/ocrad/ -r</action> + <action type="shell_command">rm $INSTALL_DIR/cuneiform/ -r</action> + + <action type="set_environment"> + <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$GRAPHICSMAGICK_ROOT_DIR/lib/</environment_variable> + <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/potrace/build/lib/</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <!-- OSRA_DATA_FILES is only used by the galaxy wrapper and is not part of OSRA --> + <environment_variable name="OSRA_DATA_FILES" action="set_to">$INSTALL_DIR/share</environment_variable> + </action> + </actions> + </install> + <readme>We still have a handfull of requirements</readme> + </package> +</tool_dependency> |