<?xml version="1.0"?>
<tool_dependency>
  <package name="samtools" version="0.1.16">
    <install version="1.0">
      <actions_group>
        <actions os="linux" architecture="i386">
          <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action>
          <action type="move_directory_files">
            <source_directory>.</source_directory>
            <destination_directory>$INSTALL_DIR</destination_directory>
          </action>
        </actions>
        <actions os="linux" architecture="x86_64">
          <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action>
          <action type="move_directory_files">
            <source_directory>.</source_directory>
            <destination_directory>$INSTALL_DIR</destination_directory>
          </action>
        </actions>
        <actions os="darwin" architecture="i386">
          <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action>
          <action type="move_directory_files">
            <source_directory>.</source_directory>
            <destination_directory>$INSTALL_DIR</destination_directory>
          </action>
        </actions>
        <actions os="darwin" architecture="x86_64">
          <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action>
          <action type="move_directory_files">
            <source_directory>.</source_directory>
            <destination_directory>$INSTALL_DIR</destination_directory>
          </action>
        </actions>
        <actions>
          <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action>
          <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
          <action type="shell_command">make</action>
          <action type="move_file">
            <source>samtools</source>
            <destination>$INSTALL_DIR/bin</destination>
          </action>
          <action type="move_file">
            <source>libbam.a</source>
            <destination>$INSTALL_DIR/lib</destination>
          </action>
        </actions>
        <action type="set_environment">
          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
          <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
        </action>
      </actions_group>
    </install>
        <readme>
          This is the last version of SAMTools to include the 'pileup' command.
          
          Program: samtools (Tools for alignments in the SAM format)
          Version: 0.1.16 (r963:234)
          
          Usage:   samtools &lt;command&gt; [options]
          
          Command: view        SAM&lt;-&gt;BAM conversion
         sort        sort alignment file
         pileup      generate pileup output
         mpileup     multi-way pileup
         depth       compute the depth
         faidx       index/extract FASTA
         tview       text alignment viewer
         index       index alignment
         idxstats    BAM index stats (r595 or later)
         fixmate     fix mate information
         glfview     print GLFv3 file
         flagstat    simple stats
         calmd       recalculate MD/NM tags and '=' bases
         merge       merge sorted alignments
         rmdup       remove PCR duplicates
         reheader    replace BAM header
         cat         concatenate BAMs
         targetcut   cut fosmid regions (for fosmid pool only)
         phase       phase heterozygotes
        </readme>
  </package>
</tool_dependency>