Mercurial > repos > devteam > package_bwa_0_5_9

annotate tool_dependencies.xml @ 1:0eb3d3c40344

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Uploaded updated tool dependency definition specifiying precompiled binaries.
author devteam
date Tue, 17 Dec 2013 09:20:31 -0500
parents 7959322e3f4b
children ec2595e4d313
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7959322e3f4b Uploaded tool_dependencies.xml
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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="0.5.9">
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4 <install version="1.0">
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5 <actions_group>
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6 <actions architecture="i386" os="linux">
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7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/bwa/bwa-0.5.9-Linux-i686.tgz</action>
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8 <action type="move_directory_files">
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9 <source_directory>.</source_directory>
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10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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11 </action>
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12 </actions>
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13 <actions architecture="x86_64" os="linux">
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14 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/bwa/bwa-0.5.9-Linux-x86_64.tgz</action>
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15 <action type="move_directory_files">
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16 <source_directory>.</source_directory>
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17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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18 </action>
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19 </actions>
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20 <actions architecture="x86_64" os="darwin">
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21 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/bwa/bwa-0.5.9-Linux-x86_64.tgz</action>
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22 <action type="move_directory_files">
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23 <source_directory>.</source_directory>
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24 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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25 </action>
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26 </actions>
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27 <actions>
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28 <action type="download_by_url">http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2</action>
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29 <action type="shell_command">make</action>
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30 <action type="move_file">
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31 <source>bwa</source>
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32 <destination>$INSTALL_DIR/bin</destination>
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33 </action>
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34 </actions>
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35 <action type="set_environment">
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36 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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37 </action>
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38 </actions_group>
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39 </install>
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40 <readme>
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41 This is the last version of BWA that uses separate files for BWT and reverse BWT.
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42
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43 Program: bwa (alignment via Burrows-Wheeler transformation)
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44 Version: 0.5.9-r16
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45 Contact: Heng Li &lt;lh3@sanger.ac.uk&gt;
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46
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47 Usage: bwa &lt;command&gt; [options]
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48
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49 Command: index index sequences in the FASTA format
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50 aln gapped/ungapped alignment
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51 samse generate alignment (single ended)
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52 sampe generate alignment (paired ended)
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53 bwasw BWA-SW for long queries
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55 fa2pac convert FASTA to PAC format
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56 pac2bwt generate BWT from PAC
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57 pac2bwtgen alternative algorithm for generating BWT
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58 bwtupdate update .bwt to the new format
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59 pac_rev generate reverse PAC
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60 bwt2sa generate SA from BWT and Occ
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61 pac2cspac convert PAC to color-space PAC
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62 stdsw standard SW/NW alignment
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63 </readme>
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64 </package>
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65 </tool_dependency>