Mercurial > repos > iuc > package_mummer_3_23
view tool_dependencies.xml @ 0:cc6c4d6ebceb draft
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
author | iuc |
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date | Thu, 22 May 2014 08:44:10 -0400 |
parents | |
children | 9ddc606546c3 |
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<?xml version="1.0"?> <tool_dependency> <package name="mummer" version="3.23"> <install version="1.0"> <actions> <action type="download_by_url">http://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> </action> <action type="shell_command"> cd $INSTALL_DIR; make; </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> http://mummer.sourceforge.net/ MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences. </readme> </package> </tool_dependency>