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annotate tool_dependencies.xml @ 21:f509cd1d5a78 draft

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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fd1625359a101d8a6b0b8d97028cc8be509398f2\n'-dirty
author nick
date Thu, 04 Jan 2018 23:55:06 -0500
parents e5d1d90c099b
children e875e5572808
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="bowtie" version="1.1.2">
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4 <repository changeset_revision="8584a4574ab1" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="mafft" version="7.221">
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7 <repository changeset_revision="dd4a533a0e3c" name="mafft" owner="rnateam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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075ef42d1ce5 Bugfix in kalign for very diverse read lengths.
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9 <package name="networkx" version="1.10">
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91170668e6b4 Temporary fix for networkx dependency for conda.
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10 <repository changeset_revision="3469a6858fd4" name="package_networkx_1_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="dunovo" version="2.0.10">
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13 <install version="1.0">
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14 <actions>
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15 <!-- download the main dunovo package files -->
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16 <action sha256sum="81ef826b54746f4335f400b0ec5580bf04b5edfd8051682a684717fb32246227" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.10.tar.gz</action>
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17 <!-- download the utillib submodule -->
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18 <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action>
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19 <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action>
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20 <action type="shell_command">rm v0.1.0.tar.gz</action>
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21 <action type="move_file">
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22 <source>utillib-0.1.0</source>
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23 <destination>utillib</destination>
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24 </action>
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25 <!-- download the kalign submodule -->
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26 <action type="download_file">https://github.com/makrutenko/kalign-dunovo/archive/v0.2.0.tar.gz</action>
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27 <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
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28 <action type="shell_command">rm v0.2.0.tar.gz</action>
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29 <action type="move_file">
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30 <source>kalign-dunovo-0.2.0</source>
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31 <destination>kalign</destination>
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32 </action>
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33 <!-- download the ET submodule -->
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34 <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action>
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35 <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action>
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36 <action type="shell_command">rm v0.2.2.tar.gz</action>
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37 <action type="move_file">
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38 <source>ET-0.2.2</source>
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39 <destination>ET</destination>
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40 </action>
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41 <!-- make and install -->
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42 <action type="shell_command">make clean</action>
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43 <action type="shell_command">make</action>
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44 <action type="move_directory_files">
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45 <source_directory>.</source_directory>
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46 <destination_directory>$INSTALL_DIR</destination_directory>
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47 </action>
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48 <action type="set_environment">
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49 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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50 </action>
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51 </actions>
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52 </install>
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53 </package>
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54 </tool_dependency>