qixnat - XNAT facade¶
Synopsis¶
qixnat provides a XNAT facade.
API: | http://qixnat.readthedocs.org/en/latest/api/index.html |
---|---|
Git: | https://github.com/ohsu-qin/qixnat |
Installation¶
qixnat
depends on the pyxnat module, which can in turn can be tricky to
install. Furthermore, the pyxnat installation guide is itself insufficient
to install pyxnat dependencies consistently in all environments. Consequently,
the following installation steps must be followed to ensure a correct build:
On Linux only, install the
libxslt
dev package. For Ubuntu or other Debian-based systems, execute:sudo aptitude install libxslt-dev
For Red Hat, execute:
sudo yum install libxslt-dev
Anaconda is recommended for ensuring package and library consistency. Install Anaconda in
$HOME/anaconda
on your workstation according to the Anaconda Installation Instructions. Preferably, install the Anaconda Accelerate add-on as well. Note that a Anaconda Accelerate Academic User License is available.Add
$HOME/anaconda/bin
to your PATH, if necessary:export PATH=$HOME/anaconda/bin:$PATH
Make an Anaconda virtual environment initialized with
pip
, e.g.:conda create --name qin pip
Activate the Anaconda environment, e.g.:
source activate qin
As a convenience, you can initialize this environment at login by prepending Anaconda and your virtual environment to
PATH
in your shell login script. E.g., for Linux or Mac OS X, open an editor on$HOME/.bashrc
or$HOME/.bash_profile
and add the following lines:# Prepend the Anaconda base applications. export PATH=$HOME/anaconda/bin:$PATH # Prepend the virtual environment. source activate qin
and refresh your environment:
. $HOME/.bash_profile
Install the
qixnat
dependencies hosted by Anaconda:wget -q --no-check-certificate -O \ - https://www.github.com/ohsu-qin/qixnat/raw/master/requirements_conda.txt \ | xargs conda install --yes
On Mac only, reinstall the lxml package using the
-f
force option to work around a lxml install issue:conda install -f lxml
Install the
qixnat
package:pip install qixnat
Usage¶
Run the following command for the utility options:
cpxnat --help
lsxnat --help
rmxnat --help
The primary read API interface of interest is the XNAT facade class.