Install supporting packages¶

Using the Required Supporting Packages table below, install any missing prerequisite packages by following the instructions for your specific Linux distribution.

For example, SUSE users can use YaST to install them; RedHat and CentOS users can use yum, Debian and Ubuntu uses apt-get.

We highly recommend using pre-built binary packages to install the programs. Installing from source can quickly become a nightmare! See also the previous page, Instructions_for_installing_CentOS_on_your_computer for Red Hat based systems.

Required supporting packages:¶

Name:	Download site:	yum package name	SuSE rpm name	Debian 8 package name
Python 2.7 or newer	http://www.python.org	python	python-devel	python
wxPython 2.5.2.8 or newer	http://www.wxpython.org	wxPython	python-wxGTK	python-wxgtk3.0
Python Imaging Library (PIL) fork Pillow *	https://pillow.readthedocs.io/en/stable/	python-pillow	python-pillow	python-pillow
NumPy 1.0.1 or newer	http://numpy.scipy.org/	numpy	numpy	python-numpy
SciPy 0.5.1 (tested, others may work)*	http://www.scipy.org	scipy	python-scipy	python-scipy

PyMySQL:

pip install PyMySQL==0.10.1

Appion Only (3.2)

Name:	Download site:	SuSE rpm name	Debian 8 package name
joblib 0.8.3-r1 or newer	https://pypi.python.org/pypi/joblib	python-joblib	python-joblib

joblib can be installed with the command

easy_install joblib==0.10.3

• The specific version is compatible with python 2.6 on CentOS 6
• If python 2.7 is used, the version does not need to be specified.

If that does not work because the version is not found. Try this on CentOS6

yum install python-pip
pip install joblib==0.10.3

Appion trunk only¶

Name:	Download site:	yum package name	SuSE rpm name	Debian 8 package name
h5py		h5py	python-h5py	python-h5py

• disable the archive rpmforge before reinstall if seeing error on import:
  

  ImportError: libhdf5.so.6: cannot open shared object file: No such file or directory
  

  
  See https://www.centos.org/forums/viewtopic.php?t=46181
  and
  http://kbfaq.blogspot.com/2011/08/installing-rpmforge-repository.html

For CentOS, see Download additional Software page, if you have trouble finding these packages.

Scipy/Numpy¶

SUSE specific issues¶

• SciPy may not build from source properly on some versions of SuSE due to an incompatible LAPACK package that comes with SuSE. You can get scipy as well as a compatible LAPACK etc. from http://repos.opensuse.org/science (need to specify your SuSE version and machine etc.)
• See also https://bugzilla.redhat.com/show_bug.cgi?id=489887 regarding LD_LIBRARY_PATH restriction to LAPACK installation.

You can test your numpy and scipy install with their build in test functions:

python -c 'import numpy; numpy.test(level=1)'
python -c 'import scipy; scipy.test(level=1)'

Numpy is more stable should be successful. Expect to see lots of errors with scipy.

Mac OS X 10.5+:¶

You can successfully install most of these packages on a Mac by downloading DMG files and clicking on the install programs. This is not for novice Mac user. Be warned, wxpython problems on Mac will make your life difficult in using Leginon gui. Don't make your mac the only processing server if it is Leginon that you will use mainly.

1. First, start by downloading the Mac OS X Installer Disk Image (v2.6 recommended) from http://python.org/download/ and install the newer version of python
2. Download and install numpy and scipy DMG files from http://sourceforge.net/projects/numpy/files/ and http://sourceforge.net/projects/scipy/files/
3. Download and install wxPython DMG file from http://www.wxpython.org/download.php

Other program need more work:

1. The Python Imaging Library (PIL) has be compiled from source, which also requires the Mac OS X Developer tools to be installed.

Download Appion/Leginon Files >

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