Mercurial > repos > iuc > package_mummer_3_23
comparison 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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-1:000000000000 | 0:cc6c4d6ebceb |
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1 <?xml version="1.0"?> | |
2 <tool_dependency> | |
3 <package name="mummer" version="3.23"> | |
4 <install version="1.0"> | |
5 <actions> | |
6 <action type="download_by_url">http://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz</action> | |
7 <action type="move_directory_files"> | |
8 <source_directory>.</source_directory> | |
9 <destination_directory>$INSTALL_DIR</destination_directory> | |
10 </action> | |
11 <action type="shell_command"> | |
12 cd $INSTALL_DIR; make; | |
13 </action> | |
14 <action type="set_environment"> | |
15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable> | |
16 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> | |
17 </action> | |
18 </actions> | |
19 </install> | |
20 <readme> | |
21 http://mummer.sourceforge.net/ | |
22 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. | |
23 </readme> | |
24 </package> | |
25 </tool_dependency> |