Mercurial > repos > bgruening > upload_testing
diff tool_dependencies.xml @ 105:f258fbfead4b draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 11 Apr 2014 16:32:28 -0400 |
| parents | 0b732f3cfad0 |
| children | cd64faa6b531 |
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--- a/tool_dependencies.xml Thu Apr 03 06:07:32 2014 -0400 +++ b/tool_dependencies.xml Fri Apr 11 16:32:28 2014 -0400 @@ -1,74 +1,12 @@ <?xml version="1.0"?> <tool_dependency> - <package name="openbabel" version="2.3.2"> - <repository changeset_revision="8426be5149ce" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="graphicsmagick" version="1.3.18"> - <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <set_environment version="1.0"> + <environment_variable action="set_to" name="PEPTIDESHAKER_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> + <package name="searchgui" version="1.14.1"> + <repository changeset_revision="0692ca995a01" name="package_searchgui_1_14_4" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="osra" version="2.0.0"> - <install version="1.0"> - <actions> - <!-- first action is always downloading --> - <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz</action> - - <!-- populate the environment variables from the dependend repos --> - <action type="set_environment_for_install"> - <repository changeset_revision="8426be5149ce" name="package_openbabel_2_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="openbabel" version="2.3.2" /> - </repository> - <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="graphicsmagick" version="1.3.18" /> - </repository> - </action> - - <!--compiling potrace-1.11 --> - <action type="shell_command">wget http://potrace.sourceforge.net/download/potrace-1.11.tar.gz</action> - <action type="shell_command">tar xfvz potrace-1.11.tar.gz && cd potrace-1.11 && ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build && make && make install</action> - - <!--compiling gocr 0.50patched --> - <!-- not yet possible - <action type="shell_command">wget http://www-e.uni-magdeburg.de/jschulen/ocr/gocr-0.50.tar.gz</action> - <action type="shell_command">tar xfvz gocr-0.50.tar.gz && cd gocr-0.50 && ./configure -|-prefix=$INSTALL_DIR/gocr/build && make libs && make all install</action> - --> - <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action> - <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz && cd gocr-0.50pre-patched && ./configure --prefix=$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=$INSTALL_DIR/cuneiform/build/ && make && make install</action> - - <!--And finally OSRA 1.4.0--> - <!-- Extending the PATH is needed for OSRA --> - <action type="shell_command">export PATH=$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 $INSTALL_DIR/cuneiform/ -r</action> - - <action type="set_environment"> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/</environment_variable> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <!-- OSRA_DATA_FILES is only used by the galaxy wrapper and is not part of OSRA --> - <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable> - </action> - </actions> - </install> - <readme>We still have a handfull of requirements</readme> + <package name="peptide_shaker" version="0.20.1"> + <repository changeset_revision="c661fad47f03" name="package_peptideshaker_0_20_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>