<?xml version="1.0"?>
<tool_dependency>
  <package name="sra_toolkit" version="2.5.2">
    <install version="1.0">
      <actions>
        <action type="make_directory">src</action>
        <action type="make_directory">build</action>
        <action type="change_directory">src</action>
        <action type="download_by_url">https://github.com/ncbi/ncbi-vdb/archive/2.5.2.tar.gz</action>
        <action type="shell_command">
            LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
            ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
            make
            make install
        </action>
        <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
        <action type="download_by_url">https://github.com/ncbi/ngs/archive/1.1.3.tar.gz</action>
        <action type="change_directory">../src</action>
        <action type="shell_command">
            ls
            mv sra-tools-2.5.2 sra-tools
            mv ngs-1.1.3 ngs      
            mv  ncbi-vdb-2.5.2  ncbi-vdb      
            LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
            cd $INSTALL_DIR/src/ncbi-vdb
            ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
            make
            make install
            cd $INSTALL_DIR/src/ngs/ngs-sdk
            ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
            make
            make install
            cd $INSTALL_DIR/src/sra-tools
            ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build --with-ncbi-vdb-build=$INSTALL_DIR/build --with-ncbi-vdb-sources=$INSTALL_DIR/src/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR
            sed -i -e "109s/-static//" tools/copycat/Makefile
            make
            make install
            cd $INSTALL_DIR/bin
            ./vdb-config -s "/repository/user/main/public/cache-enabled=false"
            ./vdb-config -s "/repository/user/main/public/root=$INSTALL_DIR"
        </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.
This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
download of a large SRA data set.

Build Requirements:
  - make
  - git
  - gcc
  - g++
  - libxml2
  - libcurl4
  - zlib

On a debian based Linux OS use:

  apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev

    </readme>
  </package>
</tool_dependency>