Mercurial > repos > bgruening > bismark
diff tool_dependencies.xml @ 0:62c6da72dd4a draft
Uploaded
author | bgruening |
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date | Sat, 06 Jul 2013 09:57:36 -0400 |
parents | |
children | 9d02cd7883ad |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Jul 06 09:57:36 2013 -0400 @@ -0,0 +1,64 @@ +<?xml version="1.0"?> +<package name="samtools" version="0.1.18"> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_samtools_0_1_18" owner="devteam " changeset_revision="a7936f4ea405" /> +</package> +<tool_dependency> + <set_environment version="1.0"> + <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> + <package name="bowtie2" version="2.1.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>bowtie2</source> + <destination>$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> + + +