view tool_dependencies.xml @ 39:1d152e8cb375 draft

add fastq output option to sam dump

<?xml version="1.0"?>
<tool_dependency>
  <package name="sra_toolkit" version="2.3.2-4">
    <install version="1.0">
      <actions>
	<action type="download_by_url">http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.3.2-4/sra_sdk-2.3.2-4.tar.gz</action>
	<action type="shell_command">make release</action>
	<action type="shell_command">make static</action>
	<action type="shell_command">make</action>
	<action type="make_directory">$INSTALL_DIR/bin</action>	
	<action type="make_directory">$INSTALL_DIR/ncbi</action>	
	<action type="make_directory">$INSTALL_DIR/ncbi/public</action>	
	<action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" bin64/ncbi/default.kfg</action>
	<action type="shell_command">cp --recursive --dereference bin64/* $INSTALL_DIR/bin</action>
	<action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
      </actions>
    </install>
    <readme>Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. Various tools for working with SRA from NCBI.
This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
Build Requirements:
  ar 
  bash
  make
  gcc, g++
  libxml2
  libcurl4
  zlib
    </readme>
  </package>
</tool_dependency>