Mercurial > repos > bgruening > upload_testing
changeset 33:6db18ec30d4c
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 06 Jun 2013 02:33:42 -0400 |
| parents | ac172e20bf20 |
| children | 9f25296ac133 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 9 insertions(+), 55 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon May 27 13:31:52 2013 +0200 +++ b/tool_dependencies.xml Thu Jun 06 02:33:42 2013 -0400 @@ -1,64 +1,18 @@ +<?xml version="1.0"?> <tool_dependency> - <package name="openbabel" version="2.3.2"> - <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/" /> - </package> - <package name="osra" version="2.0.0"> + <package name="fastqc_dist_0_10_1" version="0.10.1"> <install version="1.0"> <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz</action> - - <action type="set_environment_for_install"> - <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/"> - <package name="graphicsmagick" version="1.3.18" /> - </repository> - </action> - <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=$INSTALL_DIR/potrace/build && make && make install</action> - - <action type="shell_command">wget http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action> - <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz && cd gocr-0.50pre-patched && ./configure --prefix=$INSTALL_DIR/gocr/build && make libs && make all install</action> - - - - <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=$INSTALL_DIR/tclap/build && make && make install</action> - - - <action type="shell_command">wget http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action> - <action type="shell_command">tar xfvz ocrad-0.21.tar.gz && cd ocrad-0.21 && ./configure --prefix=$INSTALL_DIR/ocrad/build && make && make install</action> - - - <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=$INSTALL_DIR/cuneiform/build/ && make && make install</action> - - - - <action type="shell_command">export PATH=$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/gocr/ -r</action> - <action type="shell_command">rm $INSTALL_DIR/ocrad/ -r</action> - <action type="shell_command">rm $INSTALL_DIR/cuneiform/ -r</action> - + <action type="download_by_url">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip</action> + <action type="move_directory_files"> + <source_directory>../FastQC</source_directory> + <destination_directory>$INSTALL_DIR/fastqc_dist</destination_directory> + </action> + <action type="shell_command">chmod ugo+x $INSTALL_DIR/fastqc_dist/fastqc</action> <action type="set_environment"> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$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> - - <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/fastqc_dist</environment_variable> </action> </actions> </install> - <readme>We still have a handfull of requirements</readme> </package> </tool_dependency>