Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

annotate tool_dependencies.xml @ 28:b355098dc1f6 draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 9ab15e03577fc2e1204deb451ec2f434862c970f
author pjbriggs
date Mon, 01 Oct 2018 05:10:52 -0400
parents b5e43dfe07ac
children 3512b135ecb0
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="amplicon_analysis_pipeline" version="1.2.3">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">https://github.com/MTutino/Amplicon_analysis/archive/v1.2.3.tar.gz</action>
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7 <action type="move_file">
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8 <source>Amplicon_analysis_pipeline.sh</source>
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9 <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
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10 </action>
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11 <action type="move_file">
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12 <source>FIRST_STEP.sh</source>
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13 <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
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14 </action>
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15 <action type="move_file">
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16 <source>VSEARCH.sh</source>
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17 <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
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18 </action>
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19 <action type="move_file">
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20 <source>STAT_ANALYSIS.sh</source>
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21 <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
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22 </action>
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23 <action type="move_file">
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24 <source>THIRD_STEP.sh</source>
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25 <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
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26 </action>
13
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27 <action type="move_directory_files">
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28 <source_directory>uc2otutab</source_directory>
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29 <destination_directory>$INSTALL_DIR/Amplicon_analysis_pipeline/uc2otutab</destination_directory>
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30 </action>
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31 <action type="set_environment">
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32 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/Amplicon_analysis_pipeline</environment_variable>
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33 </action>
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34 </actions>
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35 </install>
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36 </package>
21
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37 <!--
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38 microbiomeutil provides ChimeraSlayer
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39 -->
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40 <package name="microbiomeutil-chimeraslayer" version="2010-04-29">
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41 <install version="1.0">
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42 <actions>
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43 <action type="download_by_url">https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz</action>
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44 <action type="move_directory_files">
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45 <source_directory>ChimeraSlayer</source_directory>
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46 <destination_directory>$INSTALL_DIR/ChimeraSlayer</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">$INSTALL_DIR/ChimeraSlayer</environment_variable>
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50 </action>
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51 </actions>
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52 </install>
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53 </package>
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54 <!--
21
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55 uclust required for QIIME/pyNAST
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56 License only allows this version to be used with those two packages
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57 See:
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58 http://drive5.com/uclust/downloads1_2_22q.html
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59 -->
19
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60 <package name="uclust-qiime" version="1.2.22">
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61 <install version="1.0">
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62 <actions>
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63 <action type="download_by_url">http://drive5.com/uclust/uclustq1.2.22_i86linux64</action>
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64 <action rename_to="uclust" type="move_file">
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65 <source>uclustq1.2.22_i86linux64</source>
19
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66 <destination>$INSTALL_DIR/bin</destination>
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67 </action>
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68 <action type="chmod">
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69 <file mode="755">$INSTALL_DIR/bin/uclust</file>
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70 </action>
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71 <action type="set_environment">
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72 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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73 </action>
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74 </actions>
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75 </install>
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76 </package>
6
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77 <package name="R" version="3.2.1">
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78 <repository changeset_revision="77d439695328" name="package_r_3_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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79 </package>
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80 </tool_dependency>