view tool_dependencies.xml @ 15:c71031b17e08

Avoid relative paths, and rename "ncbi" dir
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 15:05:20 -0400
parents ef71f5982df5
children dd337a830b5c
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<?xml version="1.0"?>
<tool_dependency>
  <package name="sra_toolkit" version="2.4.5">
    <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="shell_command">git clone https://github.com/ncbi/sra-tools.git</action>
        <action type="shell_command">git clone https://github.com/ncbi/ncbi-vdb.git</action>
        <action type="shell_command">git clone https://github.com/ncbi/ngs.git</action>
        <action type="shell_command">LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib</action>
        <action type="change_directory">ncbi-vdb</action>
        <action type="shell_command">git checkout bf5ffdd</action>
        <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
        <action type="change_directory">../ngs</action>
        <action type="shell_command">git checkout 3a7a0ed</action>
        <action type="change_directory">ngs-sdk</action>
        <action type="autoconf">--prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build</action>
        <action type="change_directory">../../sra-tools</action>
        <action type="shell_command">git checkout 4ef7ea0</action>
        <action type="autoconf">--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=$INSTALL_DIR --with-magic-prefix=/dev/null</action>
        <action type="shell_command">sed -i -e "s|\$(HOME)|$INSTALL_DIR|g" -e "s|cache-enabled = \"true\"|cache-enabled = \"false\"|" $INSTALL_DIR/ncbi/default.kfg</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>