Mercurial > repos > cmonjeau > package_bwa_0_6_2

annotate tool_dependencies.xml @ 0:5042c61de5c3 draft default tip

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Imported from capsule None
author cmonjeau
date Fri, 05 Jun 2015 11:41:09 -0400
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="bwa" version="0.6.2">
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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://downloads.sourceforge.net/project/bio-bwa/bwa-0.6.2.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>bwa</source>
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10 <destination>$INSTALL_DIR/bin</destination>
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11 </action>
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12 <action type="set_environment">
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13 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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14 </action>
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15 </actions>
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16 </install>
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17 <readme>
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18 Program: bwa (alignment via Burrows-Wheeler transformation)
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19 Version: 0.6.2-r126
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20 Contact: Heng Li &lt;lh3@sanger.ac.uk&gt;
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21
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22 Usage: bwa &lt;command&gt; [options]
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23
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24 Command: index index sequences in the FASTA format
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25 aln gapped/ungapped alignment
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26 samse generate alignment (single ended)
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27 sampe generate alignment (paired ended)
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28 bwasw BWA-SW for long queries
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29
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30 fa2pac convert FASTA to PAC format
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31 pac2bwt generate BWT from PAC
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32 pac2bwtgen alternative algorithm for generating BWT
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33 bwtupdate update .bwt to the new format
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34 pac_rev generate reverse PAC
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35 bwt2sa generate SA from BWT and Occ
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36 pac2cspac convert PAC to color-space PAC
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37 stdsw standard SW/NW alignment
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38 </readme>
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39 </package>
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40 </tool_dependency>