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 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
author iuc
date Sat, 10 Oct 2015 14:53:20 -0400
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c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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1 <?xml version="1.0"?>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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2 <tool_dependency>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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3 <package name="hisat" version="2.0">
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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4 <install version="1.0">
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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5 <actions_group>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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6 <actions architecture="x86_64" os="linux">
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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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>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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8 <action type="move_directory_files">
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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9 <source_directory>.</source_directory>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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11 </action>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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12 </actions>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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13 <actions architecture="x86_64" os="darwin">
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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14 <action type="download_by_url">http://ccb.jhu.edu/software/hisat2/downloads/hisat2-2.0.0-beta-OSX_x86_64.zip</action>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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15 <action type="move_directory_files">
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16 <source_directory>.</source_directory>
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17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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18 </action>
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19 </actions>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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20 <actions>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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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>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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22 <action type="shell_command">make</action>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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23 <action type="move_directory_files">
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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24 <source_directory>.</source_directory>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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25 <destination_directory>$INSTALL_DIR/bin</destination_directory>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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26 </action>
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27 </actions>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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28 <action type="set_environment">
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29 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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30 <environment_variable action="set_to" name="HISAT2_ROOT_DIR">$INSTALL_DIR</environment_variable>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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31 </action>
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32 </actions_group>
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33 </install>
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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>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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35 </package>
c65f00072e57 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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36 </tool_dependency>