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annotate tool_dependencies.xml @ 9:fa563fa9b330 draft

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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty
author nick
date Fri, 23 Mar 2018 22:26:23 -0400
parents 658eefb99fd7
children 9dc43bf7d1db
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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="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.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="c5908940967d" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
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8 </package>
6
23f5d9316694 Bugfix in kalign for very diverse read lengths.
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9 <package name="networkx" version="1.10">
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5fbeaa41b223 Update to Du Novo 2.0.6.
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10 <repository changeset_revision="e761775277c1" name="package_networkx_1_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="dunovo" version="2.14">
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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="e517a12794e7cac31b4ebcad99e6a6c0789027ace7d33f89d06ff2bc961515fc" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.14.tar.gz</action>
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17 <!-- TODO: Store dunovo version number in variable instead of hardcoding it everywhere. -->
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18 <!-- Move precheck.py and its dependencies into the main source directory. -->
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19 <action type="move_file">
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20 <source>utils/precheck.py</source>
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21 <destination>$TMP_WORK_DIR/dunovo-2.14</destination>
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22 </action>
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23 <action type="move_file">
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24 <source>utils/getreads.py</source>
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25 <destination>$TMP_WORK_DIR/dunovo-2.14</destination>
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26 </action>
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27 <!-- install submodules -->
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28 <action type="shell_command">rmdir kalign utillib ET</action>
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29 <!-- download the utillib submodule -->
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30 <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action>
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31 <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action>
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32 <action type="shell_command">rm v0.1.0.tar.gz</action>
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33 <action rename_to="utillib" type="move_file">
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34 <source>utillib-0.1.0</source>
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35 <destination>$TMP_WORK_DIR/dunovo-2.14</destination>
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36 </action>
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37 <!-- download the kalign submodule -->
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38 <action type="download_file">https://github.com/makrutenko/kalign-dunovo/archive/v0.2.0.tar.gz</action>
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39 <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
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40 <action type="shell_command">rm v0.2.0.tar.gz</action>
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41 <action rename_to="kalign" type="move_file">
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42 <source>kalign-dunovo-0.2.0</source>
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43 <destination>$TMP_WORK_DIR/dunovo-2.14</destination>
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44 </action>
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45 <!-- download the ET submodule -->
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46 <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action>
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47 <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action>
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48 <action type="shell_command">rm v0.2.2.tar.gz</action>
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49 <action rename_to="ET" type="move_file">
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50 <source>ET-0.2.2</source>
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51 <destination>$TMP_WORK_DIR/dunovo-2.14</destination>
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52 </action>
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53 <!-- make and install -->
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54 <action type="shell_command">make clean</action>
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55 <action type="shell_command">make</action>
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56 <action type="move_directory_files">
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57 <source_directory>.</source_directory>
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58 <destination_directory>$INSTALL_DIR</destination_directory>
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59 </action>
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60 <action type="set_environment">
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61 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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62 </action>
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63 </actions>
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64 </install>
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65 </package>
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66 </tool_dependency>