Aqua-Duct installation guide¶
Aqua-Duct software is software written in Python (CPython) and comprises of two elements:
- aquaduct - a Python package,
- valve - a script that uses
aquaductto perform calculations.
You can download Aqua-Duct packages directly from Aqua-Duct homepage. This page includes older versions of Aqua-Duct as well as development version.
If you follow this installation guide you will install current release.
If you encounter any problems with installation do not hesitate to contact us at firstname.lastname@example.org. We are REALLY willing to help!
Please, provide us with us much info as you can. In particular try to include following information:
- Operating system’s name and version, and CPU architecture (if relevant).
- Python version.
- Command(s) you have used for installation.
- Any error/warning/info message(s) that emerged during or after installation.
- Python 2.7 (CPython implementation)
Aqua-Duct should work on every machine on which you can install the above mentioned software. On computers older then 10 years it may work very slow though. We recommend 64bit SMP architecture, with at least 4GB RAM (32 GB RAM is recommended).
Generic Python installation¶
The easiest way to install Aqua-Duct is to install Python 2.7 and use following command:
pip install aquaduct
If pip is not available try to install it by typing:
Depending on the settings of your system you can prepend the above command with sudo or doas or do user installation:
# sudo sudo pip install aquaduct # doas doas pip install aquaduct # 'user' installation pip install aquaduct --user
It is also good idea to try to install Aqua-Duct using virtualenv:
virtualenv aquaduct_installation cd aquaduct_installation . bin/activate pip install aquaduct
Installation of PyMOL¶
Under most modern GNU/Linux distributions PyMOL is available as a package in repositories. For example if you are under Ubuntu/Debian you can install it by following command:
sudo apt-get install pymol
Under Windows there are several ways to install PyMOL, for more details see PyMOL web site.
Instructions for macOS and OpenBSD are in appropriate sections below.
Installation was tested on limited number of GNU/Linux systems. On the most of modern installations you can simply follow generic instructions, for example under Ubuntu 16.04 you can type:
sudo pip install aquaduct
NetCDF4 & MDAnalysis installation Ubuntu 14.04¶
Other systems may require additional work, in particular installation of NetCDF4 is sometimes cumbersome. Following is an example how to install all required packages under Ubuntu 14.04:
# install required python packages sudo apt-get install python-dev python-pip python-numpy python-scipy python-matplotlib python-scikits-learn # install necessary libraries and git - all required to compile netCDF4 sudo apt-get -y install libnetcdf-dev libhdf5-dev git # clone netcdf4 python repository git clone https://github.com/Unidata/netcdf4-python.git # cd to cloned repository cd netcdf4-python # modify setup.cfg to add paths of hdf5 and netcdf4 libraries sed -i '/\[directories\]/a \ HDF5_dir = /usr/lib \ HDF5_libdir = /usr/lib \ HDF5_incdir = /usr/include \ netCDF4_dir = /usr/lib \ netCDF4_libdir = /usr/lib \ netCDF4_incdir = /usr/include' setup.cfg # run setup.py sudo python setup.py install # install MDAnalysis sudo pip install "MDAnalysis[amber]>=0.15"
If everything went fine you can follow generic instructions.
SciPy update and Ubuntu/Debian¶
Debian (and Ubuntu) uses strange approach to Python installation. To install newer version of SciPy (if required) try following procedure:
# install libraries required for SciPy compilation apt-get build-dep python-scipy # install SciPy easy_install-2.7 --upgrade scipy
The above procedure will remove current SciPy from easy-install.pth file.
Aqua-Duct installation was tested on macOS Sierra and is quite straightforward. It can be installed either with existing system Python or with custom Python installation. In both cases one have to install Xcode for the App Store.
System native Python¶
sudo easy_install pip sudo pip install aquaduct
The drawback of using system Python installation is a lack of PyMOL. It should be, however, relatively easy to compile PyMOL on your own. Try to follow compilation instruction under BSD systems.
This is recommended way of Aqua-Duct installation. If you do not have custom Python installation you can get it by using one of package managers available for macOS, for example homebrew. With this package manager you can do following:
brew install python sudo easy_install pip sudo pip install aquaduct
Next, you can install PyMOL:
brew install pymol brew cask install xquartz
Once XQuartz is installed you should reboot. The above procedure installs PyMOL, however, PyMOL Python modules are not visible. To fix it you can issue following commands:
cd /usr/local/lib/python2.7/site-packages sudo ln -s /usr/local/Cellar/pymol/*/libexec/lib/python2.7/site-packages/* ./
The above instruction assumes that you are using brew and you have only one PyMOL installation.
Installation under Windows is also possible. The limiting factor is MDAnalysis which is not officially available under Windows yet. You can, however, install Cygwin and perform Aqua-Duct installation in Cygwin.
First, start with Cygwin installation. During the setup select following packages:
- python (2.7)
- python-devel (2.7)
Another key component that have to be installed is C, C++ and Fortran compilers. You can simply install gcc-g++ and gcc-fortran packages as a first choice, select following packages:
Once Cygwin is installed with all required libraries you can perform following steps:
# install pip easy_install-2.7 pip
First, try to install SciPy:
# install SciPy pip install scipy
If you encounter any problems related to missing xlocale.h header file try the following workaround:
# prepare fake xlocale.h ln -s /usr/include/locale.h xlocale.h export CFLAGS="I"$( pwd ) # install SciPy pip install scipy
The above procedure for SciPy installation might not be optimal. For more information please got to SciPy web page.
Now, install scikit-learn and then Aqua-Duct:
# install scikit-learn pip install scikit-learn # finally, install aquaduct pip install aquaduct
Aqua-Duct can be also installed under OpenBSD (5.9 and 6.0 amd64). NetCDF-c version 4 has to be installed as OpenBSD ships only netCDF in version 3. First, install hdf5 library and GNU make:
# install hdf5 and GNU make pkg_add hdf5 gmake
Next, download netCDF sources. Version 126.96.36.199 works out of the box but is a bit outdated. Visit NetCDF web page and select version of your choice. Older versions are available in the FTP archive. Once netCDF is downloaded and extracted go to the source directory and try following procedure:
# set LD and CPP flags export LDFLAGS=-L/usr/local/lib export CPPFLAGS=-I/usr/local/include # configure project ./configure --enable-shared --enable-dap --disable-doxygen --enable-netcdf-4 --prefix=/path/to/netCDF4/lib # make and install gmake gmake install
You may now install py-scipy package:
Install pip if it is missing:
Install netCDF4 Python:
# define netcdf-4 installation directory export NETCDF4_DIR=/path/to/netCDF4/lib pip2.7 install netCDF4
At this point you can follow generic Python instructions, type:
pip2.7 install aquaduct
PyMOL at OpenBSD¶
According to our knowledge it is possible to install PyMOL 1.4.1 and it is sufficient to work with Aqua-Duct. Go to SourceForge PyMOL download page and download, save, and extract sources.
PyMOL requires Python Mega Widgets. Download, for example Pmw 1.3.3b from SourceForge Pmw download page. Extract it and install by:
python2.7 setup.py install
TKinter (2.7) and several other packages are also required:
pkg_add python-tkinter freeglut glew png
Next, go to the extracted PyMOL sources open setup.py and modify inc_dirs variable at line 129 by adding following paths:
"/usr/X11R6/include/freetype2", "/usr/X11R6/include", "/usr/local/include",
Now, you can build and install PyMOL by typing following commands:
python2.7 setup.py build python2.7 setup.py install python2.7 setup2.py install cp pymol /usr/local/bin
PyMOL can be run by typing pymol or can be used as Python module.
Installation on other BSDs might be easier. For example, Python netCDF4 is available in ports of FreeBSD and DragonFlyBSD. Try to install it and SciPy, then proceed to generic Python installation instructions.
If you are using NetBSD or other BSD try to follow OpenBSD instructions.