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.
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.
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.
-
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
-
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'
- A. Using local checkout:
-
Log in, install dependencies(if needed) and use the container while developing. To rebuild, just save the work and run the step 2 again.
The Platform SDK contains API language bindings for the following platforms:
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+.
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
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
See the Upload Agent Readme for Upload Agent build documentation.
Please contact support@dnanexus.com for any bug reports or suggestions.