view tool_dependencies.xml @ 120:2729c2326235

Fix for Rikilt issue 13 Hit e-value and identity% should be taken from the hsp with the highest bit score. Previously each of these values was calculated independently. Also use arrays for cover calculation instead of python lists and refactor the hit_info() code a bit.

<?xml version="1.0"?>
<tool_dependency>
  <package name="libxml2" version="2.9.1">
    <repository name="package_libxml2_2_9_1" owner="jankanis" prior_installation_required="True"
                toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="98807f0505f0" />
  </package>

  <package name="libxslt" version="1.1.28">
    <repository name="package_libxslt_1_1_28" owner="devteam" prior_installation_required="True"
                toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee" />
  </package>

  <package name="zlib" version="1.2.8">
    <repository name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True"
                toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="63a4a902cda2" />
  </package>

  <package name="blast2html_venv" version="0.2">
    <install version="1.0">
      <actions>
        <action type="set_environment_for_install">
          <repository name="package_libxml2_2_9_1" owner="jankanis"
                      toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="98807f0505f0">
            <package name="libxml2" version="2.9.1" />
          </repository>
          <repository name="package_libxslt_1_1_28" owner="devteam"
                      toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee">
            <package name="libxslt" version="1.1.28" />
          </repository>
          <repository name="package_zlib_1_2_8" owner="iuc"
                      toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="63a4a902cda2">
            <package name="zlib" version="1.2.8" />
          </repository>
        </action>

	<action type="setup_virtualenv">
	  jinja2==2.7.3
	  six==1.7.2
	  argparse==1.2.1
	</action>

	<!-- install lxml manually, as the setup_virtualenv action does not include the environment
	     from set_environment_for_install but shell_command does -->
	<action type="shell_command">
	  $INSTALL_DIR/venv/bin/pip install lxml==3.3.5
	</action>
	
        <action type="set_environment">
          <!-- add libxml2/zlib library paths so the runtime can find the shared libraries -->
          <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LD_LIBRARY_PATH]</environment_variable>
        </action>
      </actions>
    </install>
    <readme>A Python 2 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme>
  </package>

</tool_dependency>