Mercurial > repos > iuc > package_hisat_2_0_3

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
author iuc
date Wed, 13 Apr 2016 16:16:25 -0400
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92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
iuc
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1 <?xml version="1.0"?>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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2 <tool_dependency>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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3 <package name="hisat" version="2.0.3">
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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4 <install version="1.0">
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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5 <actions_group>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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6 <actions architecture="x86_64" os="linux">
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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7 <action type="download_by_url" sha256sum="4b32770619efcc6c14dcc9c39544cd4f7946cd286776b29965347f11f00e699d">https://depot.galaxyproject.org/software/hisat/hisat_2.0.3_linux_x64.zip</action>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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8 <action type="move_directory_files">
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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9 <source_directory>.</source_directory>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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11 </action>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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12 </actions>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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13 <actions architecture="x86_64" os="darwin">
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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14 <action type="download_by_url" sha256sum="e6bb2f06165085e6fd00408f6d1404d6875c9e58a9d3be7da966b6053789109e">https://depot.galaxyproject.org/software/hisat/hisat_2.0.3_darwin_x64.zip</action>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
iuc
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15 <action type="move_directory_files">
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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16 <source_directory>.</source_directory>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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18 </action>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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19 </actions>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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20 <actions>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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21 <action type="download_by_url" sha256sum="b2f4aa59e000d98fc57455fd83ae69f0f50992477590ca35ce834510289d552d">https://depot.galaxyproject.org/software/hisat/hisat_2.0.3_src_all.zip</action>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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22 <action type="shell_command">make</action>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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23 <action type="move_directory_files">
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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24 <source_directory>.</source_directory>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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25 <destination_directory>$INSTALL_DIR/bin</destination_directory>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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26 </action>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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27 </actions>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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28 <action type="set_environment">
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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29 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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30 <environment_variable action="set_to" name="HISAT2_ROOT_DIR">$INSTALL_DIR</environment_variable>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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31 </action>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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32 </actions_group>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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33 </install>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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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>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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35 </package>
92cab2ab7948 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 880b34df1237b56b8aa9abdd33589907498fe82f
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36 </tool_dependency>