view tool_dependencies.xml @ 23:04a9c9e8c8c3 draft

planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fd1625359a101d8a6b0b8d97028cc8be509398f2\n'-dirty

<?xml version="1.0"?>
<tool_dependency>
  <package name="bowtie" version="1.1.2">
    <repository changeset_revision="8584a4574ab1" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
  </package>
  <package name="mafft" version="7.221">
    <repository changeset_revision="dd4a533a0e3c" name="mafft" owner="rnateam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
  </package>
  <package name="networkx" version="1.10">
    <repository changeset_revision="3469a6858fd4" name="package_networkx_1_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
  </package>
  <package name="dunovo" version="2.0.10">
    <install version="1.0">
      <actions>
        <!-- download the main dunovo package files -->
        <action sha256sum="81ef826b54746f4335f400b0ec5580bf04b5edfd8051682a684717fb32246227" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.10.tar.gz</action>
        <action type="shell_command">rmdir kalign utillib ET</action>
        <!-- download the utillib submodule -->
        <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action>
        <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action>
        <action type="shell_command">rm v0.1.0.tar.gz</action>
        <action type="shell_command">ls -lFhAb &gt; /home/me/tmp/galaxy/install.ls1.log</action>
        <action type="shell_command">ls -lFhAb utillib-0.1.0 &gt; /home/me/tmp/galaxy/install.ls2.log</action>
        <action type="shell_command">echo DEBUG $TMP_WORK_DIR</action>
        <action rename_to="utillib" type="move_file">
          <source>utillib-0.1.0</source>
          <destination>$TMP_WORK_DIR</destination>
        </action>
        <action type="shell_command">ls -lFhAb &gt; /home/me/tmp/galaxy/install.ls3.log</action>
        <action type="shell_command">ls -lFhAb utillib &gt; /home/me/tmp/galaxy/install.ls4.log</action>
        <!-- download the kalign submodule -->
        <action type="download_file">https://github.com/makrutenko/kalign-dunovo/archive/v0.2.0.tar.gz</action>
        <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
        <action type="shell_command">rm v0.2.0.tar.gz</action>
        <action rename_to="kalign" type="move_file">
          <source>kalign-dunovo-0.2.0</source>
          <destination>$TMP_WORK_DIR</destination>
        </action>
        <!-- download the ET submodule -->
        <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action>
        <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action>
        <action type="shell_command">rm v0.2.2.tar.gz</action>
        <action rename_to="ET" type="move_file">
          <source>ET-0.2.2</source>
          <destination>$TMP_WORK_DIR</destination>
        </action>
        <!-- make and install -->
        <action type="shell_command">make clean</action>
        <action type="shell_command">make</action>
        <action type="shell_command">ls -lFhAb &gt; /home/me/tmp/galaxy/install.ls5.log</action>
        <action type="move_directory_files">
          <source_directory>.</source_directory>
          <destination_directory>$INSTALL_DIR</destination_directory>
        </action>
        <action type="shell_command">ls -lFhAb $INSTALL_DIR &gt; /home/me/tmp/galaxy/install.ls6.log</action>
        <action type="set_environment">
          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
        </action>
      </actions>
    </install>
  </package>
</tool_dependency>