Mercurial > repos > bgruening > upload_testing
comparison 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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| 104:0b732f3cfad0 | 105:f258fbfead4b |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="openbabel" version="2.3.2"> | 3 <set_environment version="1.0"> |
| 4 <repository changeset_revision="8426be5149ce" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> | 4 <environment_variable action="set_to" name="PEPTIDESHAKER_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> |
| 5 </set_environment> | |
| 6 <package name="searchgui" version="1.14.1"> | |
| 7 <repository changeset_revision="0692ca995a01" name="package_searchgui_1_14_4" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> | |
| 5 </package> | 8 </package> |
| 6 <package name="graphicsmagick" version="1.3.18"> | 9 <package name="peptide_shaker" version="0.20.1"> |
| 7 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> | 10 <repository changeset_revision="c661fad47f03" name="package_peptideshaker_0_20_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> |
| 8 </package> | |
| 9 <package name="osra" version="2.0.0"> | |
| 10 <install version="1.0"> | |
| 11 <actions> | |
| 12 <!-- first action is always downloading --> | |
| 13 <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz</action> | |
| 14 | |
| 15 <!-- populate the environment variables from the dependend repos --> | |
| 16 <action type="set_environment_for_install"> | |
| 17 <repository changeset_revision="8426be5149ce" name="package_openbabel_2_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> | |
| 18 <package name="openbabel" version="2.3.2" /> | |
| 19 </repository> | |
| 20 <repository changeset_revision="2fd4eb971ba5" name="package_graphicsmagick_1_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> | |
| 21 <package name="graphicsmagick" version="1.3.18" /> | |
| 22 </repository> | |
| 23 </action> | |
| 24 | |
| 25 <!--compiling potrace-1.11 --> | |
| 26 <action type="shell_command">wget http://potrace.sourceforge.net/download/potrace-1.11.tar.gz</action> | |
| 27 <action type="shell_command">tar xfvz potrace-1.11.tar.gz && cd potrace-1.11 && ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build && make && make install</action> | |
| 28 | |
| 29 <!--compiling gocr 0.50patched --> | |
| 30 <!-- not yet possible | |
| 31 <action type="shell_command">wget http://www-e.uni-magdeburg.de/jschulen/ocr/gocr-0.50.tar.gz</action> | |
| 32 <action type="shell_command">tar xfvz gocr-0.50.tar.gz && cd gocr-0.50 && ./configure -|-prefix=$INSTALL_DIR/gocr/build && make libs && make all install</action> | |
| 33 --> | |
| 34 <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action> | |
| 35 <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz && cd gocr-0.50pre-patched && ./configure --prefix=$INSTALL_DIR/gocr/build && make libs && make all install</action> | |
| 36 | |
| 37 | |
| 38 <!--compiling tclap 1.2.1 --> | |
| 39 <action type="shell_command">wget http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz</action> | |
| 40 <action type="shell_command">tar xfvz tclap-1.2.1.tar.gz && cd tclap-1.2.1 && ./configure --prefix=$INSTALL_DIR/tclap/build && make && make install</action> | |
| 41 | |
| 42 <!--compiling ocrad 0.21 --> | |
| 43 <action type="shell_command">wget http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action> | |
| 44 <action type="shell_command">tar xfvz ocrad-0.21.tar.gz && cd ocrad-0.21 && ./configure --prefix=$INSTALL_DIR/ocrad/build && make && make install</action> | |
| 45 | |
| 46 <!--compiling cuneiform 1.1.0 --> | |
| 47 <action type="shell_command">wget https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2</action> | |
| 48 <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=$INSTALL_DIR/cuneiform/build/ && make && make install</action> | |
| 49 | |
| 50 <!--And finally OSRA 1.4.0--> | |
| 51 <!-- Extending the PATH is needed for OSRA --> | |
| 52 <action type="shell_command">export PATH=$PATH:$GRAPHICSMAGICK_ROOT_DIR/bin/ && | |
| 53 ./configure --with-tclap-include=$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> | |
| 54 <action type="shell_command">make</action> | |
| 55 <action type="shell_command">make install</action> | |
| 56 | |
| 57 <action type="shell_command">rm $INSTALL_DIR/tclap/ -r</action> | |
| 58 <!--<action type="shell_command">rm $INSTALL_DIR/openbabel/ -r</action>--> | |
| 59 <action type="shell_command">rm $INSTALL_DIR/gocr/ -r</action> | |
| 60 <action type="shell_command">rm $INSTALL_DIR/ocrad/ -r</action> | |
| 61 <action type="shell_command">rm $INSTALL_DIR/cuneiform/ -r</action> | |
| 62 | |
| 63 <action type="set_environment"> | |
| 64 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/</environment_variable> | |
| 65 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable> | |
| 66 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
| 67 <!-- OSRA_DATA_FILES is only used by the galaxy wrapper and is not part of OSRA --> | |
| 68 <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable> | |
| 69 </action> | |
| 70 </actions> | |
| 71 </install> | |
| 72 <readme>We still have a handfull of requirements</readme> | |
| 73 </package> | 11 </package> |
| 74 </tool_dependency> | 12 </tool_dependency> |