SPIRE - Downloads, System Requirements, and Installation

Downloads, System Requirements, and Installation

Downloads
System requirements
Installation
The setup.py program

Spire is written in Python, and uses the Tk/Tkinter graphics library. It also requires additional Python packages.

The full installation of Spire come packaged with its own version of Python and all the required packages.

Alternatively, if your system already has the required packages, or you prefer to install them yourself, there is a smaller brief installation that only contains the Spire package.

Spire is part of the SPIDER distribution package. See the Download link at the SPIDER Home page. If you already have SPIDER installed, you can get Spire separately from the SPIDER download site.

Downloads

Spider home page: www.wadsworth.org/spider_doc/spider/docs/master.html

Spider download page: www.wadsworth.org/spider_doc/spider/download

Full Install of Spire:: spire_linux-1.5.4.tar.gz

Brief Install of Spire:: spire-1.5.3.tar.gz

System requirements

The Spire installation packages assume that you already have SPIDER and Jweb installed.

Packages required by Spire:

SPIDER (version 13 or later) www.wadsworth.org/spider_doc/spider/download

Python2.3 (or later) www.python.org/download

Tcl/Tk8.4 (or later) www.tcl.tk/software/tcltk

BLT (a Tcl plotting package) sourceforge.net/projects/blt

Python megawidgets (Pmw) sourceforge.net/projects/pmw

Python Imaging Library (PIL) www.pythonware.com/products/pil

Numpy (Python Numeric) sourceforge.net/projects/numpy

Gnuplot.py gnuplot-py.sourceforge.net

Instructions for installing these packages yourself.

Installing Spire

Full install of Spire for Linux

Obtain the compressed tar file of the Spire distribution. If the file ends in ".gz", unzip it:
gunzip spire_linux-1.5.4.tar.gz
Extract the tar file:
tar xvf spire_linux-1.5.4.tar
(or combine them): gunzip spire_linux-1.5.4.tar.gz | tar xvf
This creates the directory spire_linux-1.5.4/

Change to the Spire directory and run the script ./install.sh (be sure it starts with dot-slash!).
cd spire_linux-1.5.4
./install.sh
This creates scripts that allow you to run Spire (and Python) from the spire_linux-1.5.4/bin directory. It then call Spire's setup.py program.

Brief install of Spire

If your system already has all the prerequisite Python packages, download and extract the the small Spire distribution.
gunzip spire-1.5.3.tar.gz | tar xvf

Change to the Spire directory and run the program setup.py
cd spire-1.5.3
python setup.py

Spire's setup.py program

setup.py calls testinstall.py, which checks if you all the required packages. Then setup tries to find the commands that run SPIDER and Jweb on your system, and writes these commands to a file called Spire/LocalVars.py

Spire/LocalVars.py will have lines that look something like this:

spidercmd = '/usr/local/bin/spider'
jwebcmd = 'java -Xmx300m -Djava.util.prefs.syncInterval=2000000 StartWeb SPIDUI &'

Then setup tries to copy the Spire directory to the Python site-packages directory, spire_linux-1.5.4/lib/python2.5/site-packages (for full install), or (for the brief install) a path that may look something like: /usr/local/lib/python2.4/site-packages/Spire
For the latter case, you may need a system administrator or someone who has write permission for this directory to install Spire there.

In addition to Spire, setup.py also installs a Spider directory under site-packages. The Spider library enables you to write Python programs that can work with Spider files. See www.wadsworth.org/spider_doc/spider/docs/python/spipylib/index.html

Finally, setup will display a command to add spire-1.5.3/bin to your path. The bin directory contains useful utilites, including numerous graphical tools, which are described at the guitools page.

NB: run the graphical tool programs WITHOUT THE .PY EXTENSION, e.g., 'qview', not 'qview.py'

File layout after installation

After Spire has been installed, various files are located in the installation directory, spire_linux-1.5.4:

the bin subdirectory, with spire, and various graphical tools (qview, montage, ctfmatch, etc.),
the batchfiles subdirectory, containing batch files that are included with the Spire package.
the config subdirectory, with various configuration files.

The configuration files have location tags that point to batch files in the installation directory, e.g.,

<location>/home/user/spire-1.5.3/batchfiles/SingleParticle</location>

The configuration files that come with the spire package are XML files that tell Spire where to find the reconstruction batch files. When you start a new project, using e.g. SingleParticle.xml, Spire loads batch files from the batchfiles directory into your working project directory, so you can alter the local copies without affecting the source batch files.

To use Spire with an external database, a little more configuration is necessary.

SPIDER (version 13 or later)	www.wadsworth.org/spider_doc/spider/download
Python2.3 (or later)	www.python.org/download
Tcl/Tk8.4 (or later)	www.tcl.tk/software/tcltk
BLT (a Tcl plotting package)	sourceforge.net/projects/blt
Python megawidgets (Pmw)	sourceforge.net/projects/pmw
Python Imaging Library (PIL)	www.pythonware.com/products/pil
Numpy (Python Numeric)	sourceforge.net/projects/numpy
Gnuplot.py	gnuplot-py.sourceforge.net