comparison tool_dependencies.xml @ 21:f509cd1d5a78 draft

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

20:78542cc82cb6

<?xml version="1.0"?>
<tool_dependency>
  <package name="bowtie2" version="2.2.5">
    <repository changeset_revision="f5582ac5ba3c" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
  </package>
  <package name="samtools" version="0.1.18">
    <repository changeset_revision="f499719dad6e" name="package_samtools_0_1_18" 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="2.0.9">
    <install version="1.0">
      <actions>
        <action sha256sum="6f5295b8eae0e161ee3bd28829ca140657743c695624ffc7f467f13eab2c547c" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.9.tar.gz</action>
        <action type="shell_command">make</action>
        <action type="move_directory_files">
          <source_directory>.</source_directory>
          <destination_directory>$INSTALL_DIR</destination_directory>
        </action>
        <action type="set_environment">
          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
        </action>
        <!-- Note: This does not install the submodules.
        Functionality they provide will not be available. -->
      </actions>
    </install>
  </package>
</tool_dependency>

21:f509cd1d5a78

<?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>
        <!-- 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="move_file">
          <source>utillib-0.1.0</source>
          <destination>utillib</destination>
        </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 type="move_file">
          <source>kalign-dunovo-0.2.0</source>
          <destination>kalign</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 type="move_file">
          <source>ET-0.2.2</source>
          <destination>ET</destination>
        </action>
        <!-- make and install -->
        <action type="shell_command">make clean</action>
        <action type="shell_command">make</action>
        <action type="move_directory_files">
          <source_directory>.</source_directory>
          <destination_directory>$INSTALL_DIR</destination_directory>
        </action>
        <action type="set_environment">
          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
        </action>
      </actions>
    </install>
  </package>
</tool_dependency>