Mercurial > repos > mzeidler > virana2
view tool_dependencies.xml @ 60:7352fecc9860 draft default tip
Uploaded
author | mzeidler |
---|---|
date | Sun, 29 Sep 2013 14:31:15 -0400 |
parents | d35d6c6699e5 |
children |
line wrap: on
line source
<tool_dependency> <package name="virana_python" version="1.0"> <install version="1.0"> <actions> <action type="download_by_url">https://github.com/zeidlermicha/virana/raw/master/Virana-1.0.0.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> <action type="set_environment"> <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> </package> <package name="samtools" version="0.1.19"> <install> <actions> <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> <action type="shell_command">make</action> <action type="move_file"> <source>samtools</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> </package> <package name="bwa" version="0.7.4"> <install version="1.0"> <actions> <action type="download_by_url">http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.4.tar.bz2 </action> <action type="shell_command">make</action> <action type="move_file"> <source>bwa</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> </package> <package name="STAR" version="2.3.0" > <install version="1.0"> <actions> <action type="download_by_url">https://rna-star.googlecode.com/files/STAR_2.3.0e.tgz</action> <action type="move_file"> <source>STAR</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> </package> <package name="lastz" version="1.02.00" > <install version="1.0"> <actions> <action type="download_by_url" target_filename="lastz-distrib-1.02.00.tar.gz">http://www.bx.psu.edu/miller_lab/dist/lastz-1.02.00.tar.gz</action> <action type="shell_command">make</action> <action type="move_file"> <source>src/lastz</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="move_file"> <source>src/lastz_D</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> </package> <package name="jalview" version="2.8" > <install version="1.0"> <actions> <action type="download_by_url">https://github.com/zeidlermicha/virana/raw/master/jalview.tar.gz</action> <action type="make_directory">$GALAXYROOT/tool-data/shared/jalview</action> <action type="move_file"> <source>jalview.jar</source> <destination>$GALAXYROOT/tool-data/shared/jalview</destination> </action> <action type="move_directory_files"> <source_directory>lib</source_directory> <destination_directory>$GALAXYROOT/tool-data/shared/jalview</destination_directory> </action> </actions> </install> </package> </tool_dependency>