annotate tool_dependencies.xml @ 6:a73c48890bde draft

Version v0.02.04.5: handle large output files

<?xml version="1.0"?>
<tool_dependency>
    <package name="pal_finder" version="0.02.04">
      <install version="1.0">
	<actions>
	  <action type="download_by_url">http://sourceforge.net/projects/palfinder/files/pal_finder_v0.02.04.tar.gz</action>
	  <action type="move_file">
	    <source>pal_finder_v0.02.04.pl</source>
	    <destination>$INSTALL_DIR/bin</destination>
	  </action>
	  <action type="move_file">
	    <source>config.txt</source>
	    <destination>$INSTALL_DIR/data</destination>
	  </action>
	  <action type="move_file">
	    <source>simple.ref</source>
	    <destination>$INSTALL_DIR/data</destination>
	  </action>
	  <action type="set_environment">
	    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
	  </action>
	  <action type="set_environment">
	    <environment_variable name="PALFINDER_SCRIPT_DIR" action="set_to">$INSTALL_DIR/bin</environment_variable>
	  </action>
	  <action type="set_environment">
	    <environment_variable name="PALFINDER_DATA_DIR" action="set_to">$INSTALL_DIR/data</environment_variable>
	  </action>
	</actions>
      </install>
      <readme>pal_finder also needs Perl</readme>
    </package>
    <package name="perl" version="5.16.3">
      <install version="1.0">
        <actions>
          <!-- install perl -->
          <action type="download_by_url">http://www.cpan.org/src/5.0/perl-5.16.3.tar.gz</action>
          <action type="shell_command">./Configure -des -Dprefix=$INSTALL_DIR -Dstartperl='#!/usr/bin/env perl'</action>
          <action type="make_install" />
          <action type="set_environment">
            <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
          </action>
        </actions>
      </install>
      <readme>
        Perl 5 is a highly capable, feature-rich programming language with over 25 years of
	development:

        http://www.perl.org/
      </readme>
    </package>
    <package name="primer3_core" version="2.0.0">
      <install version="1.0">
	<actions>
	  <action type="download_by_url">https://sourceforge.net/projects/primer3/files/primer3/2.0.0-alpha/primer3-2.0.0-alpha.tar.gz</action>
	  <action type="shell_command">make -C src -f Makefile</action>
	  <action type="move_file">
	    <source>src/primer3_core</source>
	    <destination>$INSTALL_DIR/bin</destination>
	  </action>
	  <action type="set_environment">
	    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
	  </action>
	</actions>
      </install>
      <readme>primer3_core</readme>
    </package>
    <package name="biopython" version="1.65">
      <install version="1.0">
	<actions>
	  <action type="shell_command">pip install  --install-option "--prefix=$INSTALL_DIR" https://pypi.python.org/packages/source/b/biopython/biopython-1.65.tar.gz</action>
	  <action type="set_environment">
	    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable>
	    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib64/python2.7/site-packages</environment_variable>
	  </action>
	</actions>
      </install>
      <readme>BioPython 1.65</readme>
    </package>
    <package name="pandaseq" version="2.8.1">
      <install version="1.0">
	<actions>
	  <action type="download_by_url">https://github.com/neufeld/pandaseq/archive/v2.8.1.tar.gz</action>
	  <action type="shell_command">./autogen.sh</action>
	  <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
	  <action type="shell_command">make</action>
	  <action type="shell_command">make install</action>
	  <action type="set_environment">
	    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
	    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
	  </action>
	</actions>
      </install>
      <readme>PANDASeq 2.8.1

      PANDASEQ is a program to align Illumina reads, optionally
      with PCR primers embedded in the sequence, and reconstruct
      an overlapping sequence.

      https://github.com/neufeld/pandaseq
      </readme>
    </package>
</tool_dependency>