DNAnexus Upload Agent

This directory contains the source code for the DNAnexus Upload Agent (UA). The UA is a command-line program for performing fast, robust file uploads to the platform. The UA is written in C++ and runs on Linux, Mac OS X, and Windows.

Build dependencies

Before building the Upload Agent, follow the instructions in the SDK Readme for installing system build dependencies.

Building

To build the UA, simply run make ua in the dx-toolkit/src directory. This will build the ua executable in the dx-toolkit/src/ua directory. The following methods can then be used from dx-toolkit/src/ua to deploy the Upload Agent:

• make install will deposit ua in the $DNANEXUS_HOME/bin directory
• make dist will build a complete UA distribution for the current platform and place it in the dist subdirectory. On Linux, the distribution is a .tar.gz file; on Windows and OS X, there are two products: a .zip file and an installer.

The ua executable is statically linked on Linux. On Mac OS X and Windows, the executable is dynamically linked, and the necessary libraries are copied along with it.

Dependencies

The UA depends on the following libraries. They are automatically downloaded and installed when running make:

• libcurl for HTTP requests. In particular, a custom statically-linked libcurl must be built, and this relies on:
  • c-ares, an asynchronous DNS library (Ubuntu package libc-ares-dev; Mac port c-ares);
  • OpenSSL or the native Windows SSL library for HTTPS;
• various Boost libraries, including Thread, Lexical Cast, Program Options, Filesystem, System, and Regex;
• zlib for compression;
• libmagic, a library to recognize the MIME type of the input file(s) (Mac port "file")
• the dxjson and dxcpp libraries for communicating with the platform API.