view tool_dependencies.xml @ 26:f0917c340f13 draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 34034189622f4cf14edd12a4de43739c37b50730-dirty

<?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">$INSTALL_DIR/Amplicon_analysis_pipeline</environment_variable>
	  </action>
	</actions>
      </install>
  </package>
  <!--
      microbiomeutil provides ChimeraSlayer
  -->
  <package name="microbiomeutil-chimeraslayer" version="2010-04-29">
    <install version="1.0">
      <actions>
	<action type="download_by_url">https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz</action>
	<action type="move_directory_files">
	  <source_directory>ChimeraSlayer</source_directory>
	  <destination_directory>$INSTALL_DIR/ChimeraSlayer</destination_directory>
	</action>
	<action type="set_environment">
	    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/ChimeraSlayer</environment_variable>
	</action>
      </actions>
    </install>
  </package>
  <!--
      uclust required for QIIME/pyNAST
      License only allows this version to be used with those two packages
      See:
      http://drive5.com/uclust/downloads1_2_22q.html
  -->
  <package name="uclust-qiime" version="1.2.22">
    <install version="1.0">
      <actions>
	<action type="download_by_url">http://drive5.com/uclust/uclustq1.2.22_i86linux64</action>
	<action rename_to="uclust" type="move_file">
	  <source>uclustq1.2.22_i86linux64</source>
	  <destination>$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>