DNAnexus Platform SDK

To install the dx CLI and the Python SDK for your platform run python3 -m pip install dxpy

• Found a bug? See Reporting Bugs below.

Welcome to the dx-toolkit repository! This repository contains the DNAnexus API language bindings and utilities for interacting with the DNAnexus platform.

See https://documentation.dnanexus.com/ and http://autodoc.dnanexus.com/ for relevant documentation.

Installing the toolkit from source

The recommended way to install the Python SDK and dx CLI of dx-toolkit locally is with python3 -m pip install -e dx-toolkit/src/python. Any changes made within this checkout will be reflected in the pip installed version.

Building inside docker

To avoid lengthy installation of dependencies on your platform and simultaneous installations of development versions of dx-toolkit on the system, you can build dx-toolkit inside a docker container.

1. Start python:3.9-bullseye in the interactive mode, mounting the repo you are working on (<local_path_to_repo>/dx-toolkit):

   # from root folder of dx-toolkit
   docker run -v `pwd`:/dx-toolkit -w /dx-toolkit -it --rm --entrypoint=/bin/bash python:3.9-bullseye
   

2. From the interactive shell install dx-toolkit.

   • A. Using local checkout:

     python3 -m pip install src/python/ --upgrade
     

   • B. Using remote branch, in this example specified in "@master":

     python3 -m pip install --upgrade 'git+https://github.com/dnanexus/dx-toolkit.git@master#egg=dxpy&subdirectory=src/python'
     

3. Log in, install dependencies(if needed) and use the container while developing. To rebuild, just save the work and run the step 2 again.

Supported languages

The Platform SDK contains API language bindings for the following platforms:

• Python (requires Python 3.8 or higher)
• C++
• Java (requires Java 7 or higher)
• R

Build dependencies for C++ and Java

Note: There is a known incompatibility (in compiling dxcpp) when using GCC 4.7 with Boost 1.49. Please either use the GCC 4.6 series, or Boost 1.50+.

Ubuntu 22.04

sudo apt install git openjdk-11-jre-headless maven python-is-python3 python3-venv python3-dev libssl-dev libffi-dev \
  flex bison build-essential cmake libboost-all-dev curl libcurl4-openssl-dev

Ubuntu 20.04

sudo apt install git make openjdk-11-jre-headless maven python-is-python3 python3-venv libssl-dev flex bison libffi-dev libboost-all-dev curl libcurl4-openssl-dev

Upload Agent

See the Upload Agent Readme for Upload Agent build documentation.

Reporting Bugs

Please contact [email protected] for any bug reports or suggestions.