| Next changeset 1:9ddc606546c3 (2015-07-17) |
|
Commit message:
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23 |
|
added:
tool_dependencies.xml |
| b |
| diff -r 000000000000 -r cc6c4d6ebceb tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu May 22 08:44:10 2014 -0400 |
| b |
| @@ -0,0 +1,25 @@ +<?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> |