Mercurial > repos > mzeidler > virana2
view tool_dependencies.xml @ 37:7f4b1408f32d draft
Uploaded
author | mzeidler |
---|---|
date | Wed, 25 Sep 2013 08:53:00 -0400 |
parents | ff5f11d54af9 |
children | 56c39038b2a9 |
line wrap: on
line source
<tool_dependency> <package name="virana_python" version="1.0"> <install version="1.0"> <actions> <action type="shell_command">echo 'Test'</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">sed -i 's/-Werror//g' src/Makefile</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">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> </package> <package name="jalview" version="2.8" > <install version="1.0"> <actions> <action type="move_directory_files"> <source>jalview</source> <destination>$INSTALL_DIR</destination> </action> <action type="set_environment"> <environment_variable name="JALVIEW_DIR" action="prepend_to">$INSTALL_DIR</environment_variable> </action> <action type="shell_command">ls $JALVIEW_DIR</action> </actions> </install> </package> </tool_dependency>