Mercurial > repos > iuc > package_mummer_3_23
annotate tool_dependencies.xml @ 1:9ddc606546c3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mummer_3_23 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
author | iuc |
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date | Fri, 17 Jul 2015 10:38:53 -0400 |
parents | cc6c4d6ebceb |
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cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
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1 <?xml version="1.0"?> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
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2 <tool_dependency> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
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3 <package name="mummer" version="3.23"> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
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4 <install version="1.0"> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
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5 <actions> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
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6 <action type="download_by_url">http://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz</action> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
parents:
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7 <action type="move_directory_files"> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
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8 <source_directory>.</source_directory> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
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9 <destination_directory>$INSTALL_DIR</destination_directory> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
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10 </action> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
parents:
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11 <action type="shell_command"> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
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12 cd $INSTALL_DIR; make; |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
parents:
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13 </action> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
parents:
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14 <action type="set_environment"> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
parents:
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15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
parents:
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16 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
parents:
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17 </action> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
parents:
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18 </actions> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
parents:
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19 </install> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
parents:
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20 <readme> |
1
9ddc606546c3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mummer_3_23 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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21 MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. |
9ddc606546c3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mummer_3_23 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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22 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, |
9ddc606546c3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mummer_3_23 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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23 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 |
9ddc606546c3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mummer_3_23 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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24 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. |
9ddc606546c3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mummer_3_23 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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25 If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate |
9ddc606546c3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mummer_3_23 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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26 alignments based upon the six-frame translations of both input sequences. |
9ddc606546c3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mummer_3_23 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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27 |
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cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
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28 http://mummer.sourceforge.net/ |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
parents:
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29 </readme> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
parents:
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30 </package> |
cc6c4d6ebceb
Uploaded initial version developed by JJ and originally released as http://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_mummer_3_23
iuc
parents:
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31 </tool_dependency> |