Mercurial > repos > iuc > package_hisat_2_0

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
author iuc
date Fri, 09 Oct 2015 05:17:25 -0400
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0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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1 <?xml version="1.0"?>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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2 <tool_dependency>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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3 <package name="hisat" version="2.0">
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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4 <install version="1.0">
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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5 <actions_group>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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6 <actions architecture="x86_64" os="linux">
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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7 <action type="download_by_url">http://ccb.jhu.edu/software/hisat2/downloads/hisat2-2.0.0-beta-Linux_x86_64.zip</action>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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8 <action type="move_directory_files">
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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9 <source_directory>.</source_directory>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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11 </action>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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12 </actions>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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13 <actions architecture="x86_64" os="darwin">
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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14 <action type="download_by_url">http://ccb.jhu.edu/software/hisat2/downloads/hisat2-2.0.0-beta-OSX_x86_64.zip</action>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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15 <action type="move_directory_files">
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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16 <source_directory>.</source_directory>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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18 </action>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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19 </actions>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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20 <actions>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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21 <action type="download_by_url">http://ccb.jhu.edu/software/hisat2/downloads/hisat2-2.0.0-beta-source.zip</action>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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22 <action type="shell_command">make</action>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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23 <action type="move_directory_files">
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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24 <source_directory>.</source_directory>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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25 <destination_directory>$INSTALL_DIR/bin</destination_directory>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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26 </action>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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27 </actions>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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28 <action type="set_environment">
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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29 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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30 <environment_variable action="set_to" name="HISAT2_ROOT_DIR">$INSTALL_DIR</environment_variable>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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31 </action>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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32 </actions_group>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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33 </install>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
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34 <readme>HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents the general population, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).</readme>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
iuc
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35 </package>
0f7f6f91aaee planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
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36 </tool_dependency>