dx-toolkit
) includes the dx
command-line client, tools for building and debugging apps, other utilities for working with DNA data on the DNAnexus platform, and Python, Java, C++ and R bindings for working with the DNAnexus platform.pip
while newer versions use pip3
. You may want to check that your version is current, as some installs of Python also come with a version of pip..bashrc
.zshrc
dx
command-line tool and the dxpy
Python module.export ARCHFLAGS="-arch x86_64"
before pip3 install dxpy
.export PYTHONIOENCODING=UTF-8
in bash ) to avoid potential character set problems running the dx
command. dxpy and dx CLI tools are tested with Python 3.5.2.pip3 install --upgrade dxpy
to upgrade the dxpy package. Only use dx upgrade
with tarball installations described below.dx-toolkit
to a proxy, please set the HTTP_PROXY
environment variable to something like export HTTP_PROXY=hostname:port
. HTTPS_PROXY
is also supported.dx-toolkit
uses certificates installed on the system to create secure connections. If your system requires an additional TLS certificate and the dx-toolkit
doesn't appear to be using a certificate installed on your system, there are two options in order of preference. First, set the DX_CA_CERT
environment variable to the path of the PEM-encoded TLS certificate file required by your parent organization. You can also connect insecurely by avoiding certificate verification all together by setting DX_CA_CERT=NOVERIFY
.dxpy
bindings and dx
command, which will be supported until March 1, 2021.zsh
on MacOS, please update your~/.zshrc
file as followsdx-toolkit*.exe
to start the installation. Systems with Windows Defender enabled may present a warning before launching the dx-toolkit installer. If you see this warning window, click "More Info", and choose "Run Anyway". The sources for the Windows installer are here.pip install python-certifi-win32
command to install it) if you encounter the following errors during certain operations (e.g. dx head file-xxx
):ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1108)
dx upgrade
command will upgrade your DNAnexus SDK to the latest recommended version. The dx upgrade
command can also revert your dx-toolkit to a previous version.dx upgrade
without any arguments will upgrade your DNAnexus SDK to the most recent version. Alternatively, you can provide dx upgrade
with a version of the DNAnexus SDK that you would prefer to have installed on your local system.Readme.md
file in the archive for build-time dependencies and further installation instructions (or view on Github).dx
command-line tool is installed and initialized withdx login
java -jar dxCompiler.jar compile workflow_file.wdl
docker
command-line tool is required to invoke the dxCompiler inside the docker container using the run-dxcompiler-docker script