Mercurial > repos > nick > dunovo
annotate tool_dependencies.xml @ 8:658eefb99fd7 draft
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
| author | nick |
|---|---|
| date | Fri, 12 Jan 2018 19:18:41 -0500 |
| parents | e7b88ffb8294 |
| children | fa563fa9b330 |
| rev | line source |
|---|---|
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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1 <?xml version="1.0"?> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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2 <tool_dependency> |
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8
658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
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3 <package name="bowtie" version="1.1.2"> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
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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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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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5 </package> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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6 <package name="mafft" version="7.221"> |
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8
658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
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7 <repository changeset_revision="c5908940967d" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" /> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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8 </package> |
| 6 | 9 <package name="networkx" version="1.10"> |
| 4 | 10 <repository changeset_revision="e761775277c1" name="package_networkx_1_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> |
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0
f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
diff
changeset
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11 </package> |
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8
658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
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12 <package name="dunovo" version="2.0.12"> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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changeset
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13 <install version="1.0"> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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14 <actions> |
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8
658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
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15 <!-- download the main dunovo package files --> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
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16 <action sha256sum="6973f163dabf82d236982534d88b5d11573a5aa0982bf9d6236be635fb9b4e11" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.12.tar.gz</action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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17 <!-- TODO: Store dunovo version number in variable instead of hardcoding it everywhere. --> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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18 <action type="shell_command">rmdir kalign utillib ET</action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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19 <!-- download the utillib submodule --> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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20 <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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21 <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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22 <action type="shell_command">rm v0.1.0.tar.gz</action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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23 <action rename_to="utillib" type="move_file"> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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24 <source>utillib-0.1.0</source> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
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25 <destination>$TMP_WORK_DIR/dunovo-2.0.12</destination> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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26 </action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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27 <!-- download the kalign submodule --> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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28 <action type="download_file">https://github.com/makrutenko/kalign-dunovo/archive/v0.2.0.tar.gz</action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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29 <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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30 <action type="shell_command">rm v0.2.0.tar.gz</action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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31 <action rename_to="kalign" type="move_file"> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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32 <source>kalign-dunovo-0.2.0</source> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
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33 <destination>$TMP_WORK_DIR/dunovo-2.0.12</destination> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
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34 </action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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35 <!-- download the ET submodule --> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
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diff
changeset
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36 <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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37 <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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38 <action type="shell_command">rm v0.2.2.tar.gz</action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
diff
changeset
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39 <action rename_to="ET" type="move_file"> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
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40 <source>ET-0.2.2</source> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
7
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41 <destination>$TMP_WORK_DIR/dunovo-2.0.12</destination> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
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42 </action> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
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43 <!-- make and install --> |
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658eefb99fd7
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
nick
parents:
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44 <action type="shell_command">make clean</action> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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45 <action type="shell_command">make</action> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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46 <action type="move_directory_files"> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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47 <source_directory>.</source_directory> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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48 <destination_directory>$INSTALL_DIR</destination_directory> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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49 </action> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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50 <action type="set_environment"> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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51 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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52 </action> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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53 </actions> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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54 </install> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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55 </package> |
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f875256c722e
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'd00f828e5768c5fac3e382b9d12f34bbdf9019e9\n'-dirty
nick
parents:
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56 </tool_dependency> |