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annotate tool_dependencies.xml @ 10:9dc43bf7d1db draft

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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'230f018da2c0bc4eedc72e0f70eac0df1e85ebdb\n'-dirty
author nick
date Fri, 01 Jun 2018 17:55:23 -0400
parents fa563fa9b330
children
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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="2.15">
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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="1cf02bcc37cc641a20bdf5e20c2b3b98d4dccd43b1182830cb1a9e7d173d1a78" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.15.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 <!-- install submodules -->
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19 <action type="shell_command">rmdir kalign utillib ET</action>
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20 <!-- download the utillib submodule -->
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21 <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action>
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22 <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action>
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23 <action type="shell_command">rm v0.1.0.tar.gz</action>
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24 <action rename_to="utillib" type="move_file">
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25 <source>utillib-0.1.0</source>
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26 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
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27 </action>
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28 <!-- download the kalign submodule -->
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29 <action type="download_file">https://github.com/makovalab-psu/kalign-dunovo/archive/v0.2.0.tar.gz</action>
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30 <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
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31 <action type="shell_command">rm v0.2.0.tar.gz</action>
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32 <action rename_to="kalign" type="move_file">
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33 <source>kalign-dunovo-0.2.0</source>
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34 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
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35 </action>
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36 <!-- download the ET submodule -->
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37 <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action>
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38 <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action>
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39 <action type="shell_command">rm v0.2.2.tar.gz</action>
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40 <action rename_to="ET" type="move_file">
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41 <source>ET-0.2.2</source>
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42 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
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43 </action>
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44 <!-- download the bfx submodule -->
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45 <action type="download_file">https://github.com/NickSto/bfx/archive/v0.2.0.tar.gz</action>
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46 <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
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47 <action type="shell_command">rm v0.2.0.tar.gz</action>
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48 <action rename_to="bfx" type="move_file">
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49 <source>bfx-0.2.0</source>
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50 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
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51 </action>
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52 <!-- Move some source files from subdirectories into the main source directory. -->
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53 <action type="move_file">
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54 <source>utils/precheck.py</source>
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55 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
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56 </action>
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57 <action type="move_file">
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58 <source>bfx/trimmer.py</source>
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59 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
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60 </action>
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61 <action type="move_file">
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62 <source>utils/getreads.py</source>
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63 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
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64 </action>
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65 <!-- make and install -->
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66 <action type="shell_command">make clean</action>
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67 <action type="shell_command">make</action>
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68 <action type="move_directory_files">
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69 <source_directory>.</source_directory>
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70 <destination_directory>$INSTALL_DIR</destination_directory>
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71 </action>
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72 <action type="set_environment">
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73 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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74 </action>
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75 </actions>
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76 </install>
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77 </package>
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78 </tool_dependency>