Mercurial > repos > iuc > package_tabix_0_2_6

annotate tool_dependencies.xml @ 1:389d2376b60b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tabix_0_2_6 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
author iuc
date Fri, 17 Jul 2015 11:16:58 -0400
parents 3d6beba7393e
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="tabix" version="0.2.6">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2</action>
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7 <action type="shell_command">make</action>
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8 <action type="move_file">
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9 <source>tabix</source>
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10 <destination>$INSTALL_DIR/bin</destination>
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11 </action>
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12 <action type="move_file">
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13 <source>bgzip</source>
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14 <destination>$INSTALL_DIR/bin</destination>
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15 </action>
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16 <action type="set_environment">
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17 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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18 <environment_variable name="TABIX_BIN_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
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19 </action>
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20 </actions>
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21 </install>
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22 <readme>
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23 Installs tabix version 0.2.6. Available binaries: tabix, bgzip
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24 http://samtools.sourceforge.net/tabix.shtml
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25
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389d2376b60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tabix_0_2_6 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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26 Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line.
389d2376b60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tabix_0_2_6 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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27 The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing,
389d2376b60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tabix_0_2_6 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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28 tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos".
389d2376b60b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_tabix_0_2_6 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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29 Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally.
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30 </readme>
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31 </package>
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32 </tool_dependency>