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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
author devteam
date Wed, 16 Sep 2015 13:38:39 -0400
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ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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1 <?xml version="1.0"?>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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2 <tool_dependency>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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3 <package name="hisat" version="2.0">
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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4 <install version="1.0">
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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5 <actions_group>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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6 <actions architecture="x86_64" os="linux">
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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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>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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8 <action type="move_directory_files">
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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9 <source_directory>.</source_directory>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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11 </action>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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12 </actions>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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13 <actions architecture="x86_64" os="darwin">
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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14 <action type="download_by_url">http://ccb.jhu.edu/software/hisat2/downloads/hisat2-2.0.0-beta-OSX_x86_64.zip</action>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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15 <action type="move_directory_files">
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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16 <source_directory>.</source_directory>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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18 </action>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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19 </actions>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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20 <actions>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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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>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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22 <action type="shell_command">make</action>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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23 <action type="move_directory_files">
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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24 <source_directory>.</source_directory>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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25 <destination_directory>$INSTALL_DIR/bin</destination_directory>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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26 </action>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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27 </actions>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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28 <action type="set_environment">
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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29 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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30 </action>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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31 </actions_group>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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32 </install>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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33 <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>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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34 </package>
ee153209837a planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
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35 </tool_dependency>