Mercurial > repos > fcaramia > methylation_analysis_bismark
diff tool_dependencies.xml @ 14:cdb7231da7f2 draft
Uploaded
author | fcaramia |
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date | Mon, 17 Jun 2013 21:44:43 -0400 |
parents | |
children | d2ba233899b0 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jun 17 21:44:43 2013 -0400 @@ -0,0 +1,58 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment version="1.0"> + <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> + <package name="bowtie2" version="2.0.0-beta7"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-source.zip</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>bowtie2</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bowtie2-align</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bowtie2-build</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +Compiling bowtie2 requires zlib and libpthread to be present on your system. + </readme> + </package> + <package name="bowtie" version="0.12.8"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-src.zip</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>bowtie</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bowtie-inspect</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>bowtie-build</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> + <readme> + </readme> + </package> +</tool_dependency>