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annotate tool_dependencies.xml @ 7:fcadce4d9a06 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
parents 243e8f9fb75b
children
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <!-- from test tool shed-->
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4 <!--<package name="samtools" version="0.1.19">
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5 <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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6 </package>-->
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7 <!--from main tool shed-->
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82814a8a2395 added samtools 0.1.19 as dependency
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8 <package name="samtools" version="0.1.19">
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9 <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
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10 </package>
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11 <package name="bowtie2" version="2.1.0">
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12 <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
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13 </package>
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14 <!--<package name="bowtie2" version="2.1.0">
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15 <install version="1.0">
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16 <actions>
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17 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
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18 <action type="shell_command">make</action>
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19 <action type="move_file">
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20 <source>bowtie2</source>
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21 <destination>$INSTALL_DIR/bin</destination>
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22 </action>
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23 <action type="move_file">
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24 <source>bowtie2-align</source>
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25 <destination>$INSTALL_DIR/bin</destination>
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26 </action>
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27 <action type="move_file">
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28 <source>bowtie2-build</source>
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29 <destination>$INSTALL_DIR/bin</destination>
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30 </action>
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31 <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action>
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32 <action type="set_environment">
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33 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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34 </action>
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35 </actions>
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36 </install>
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37 <readme>
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38 Compiling bowtie2 requires zlib and libpthread to be present on your system.
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39 </readme>
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40 </package>-->
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41 </tool_dependency>