Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

view tool_dependencies.xml @ 19:52052235644b draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f0ee1ad05711ce1499c5e219373cca74d0aafeaf-dirty
author pjbriggs
date Tue, 03 Jul 2018 09:31:24 -0400
parents ed175a4b247f
children 8d8aad8752f9
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<?xml version="1.0"?>
<tool_dependency>
  <package name="amplicon_analysis_pipeline" version="1.2.2">
      <install version="1.0">
	<actions>
	  <action type="download_by_url">https://github.com/MTutino/Amplicon_analysis/archive/v1.2.2.tar.gz</action>
	  <action type="move_file">
	    <source>Amplicon_analysis_pipeline.sh</source>
	    <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
	  </action>
	  <action type="move_file">
	    <source>FIRST_STEP.sh</source>
	    <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
	  </action>
	  <action type="move_file">
	    <source>VSEARCH.sh</source>
	    <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
	  </action>
	  <action type="move_file">
	    <source>STAT_ANALYSIS.sh</source>
	    <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
	  </action>
	  <action type="move_file">
	    <source>THIRD_STEP.sh</source>
	    <destination>$INSTALL_DIR/Amplicon_analysis_pipeline</destination>
	  </action>
	  <action type="move_directory_files">
	    <source_directory>uc2otutab</source_directory>
	    <destination_directory>$INSTALL_DIR/Amplicon_analysis_pipeline/uc2otutab</destination_directory>
	  </action>
	  <action type="set_environment">
	    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/Amplicon_analysis_pipeline</environment_variable>
	  </action>
	</actions>
      </install>
  </package>
  <package name="uclust-qiime" version="1.2.22">
    <install version="1.0">
      <actions>
	<action type="download_by_url">http://drive5.com/uclust/uclustq1.2.22_i86linux64</action>
	<action rename_to="uclust" type="move_file">
	  <source>http://drive5.com/uclust/uclustq1.2.22_i86linux64</source>
	  <destination>$INSTALL_DIR/bin</destination>
	</action>
	<action type="chmod">
	  <file mode="755">$INSTALL_DIR/bin/uclust</file>
	</action>
	<action type="set_environment">
	    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
	</action>
      </actions>
    </install>
  </package>
  <package name="R" version="3.2.1">
    <repository changeset_revision="77d439695328" name="package_r_3_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
  </package>
</tool_dependency>