TAMO -- Tools for the Analysis of Motifs

Copyright (2005) Whitehead Institute for Biomedical Research
All Rights Reserved.  No warranty expressed or implied.
Author: David Benjamin Gordon


*****************************************************************
***                                                           ***
***               Contents                                    ***
***                                                           ***
***    Installation Instructions                              ***
***                                                           ***
***       System Requirements                                 ***
***       Step 1: setup.py                                    ***
***       Step 2: $TAMO variable                              ***
***       Step 3: Install support programs                    ***
***                                                           ***
***    Documentation                                          ***
***       http://jura.wi.mit.edu/fraenkel/TAMO/documentation/ ***
***                                                           ***
*****************************************************************

*********************************
***                           ***
***     System Requirements   ***
***                           ***
*********************************

* Python >= 2.3 (might work with 2.2, but with missing functionality)
* C/C++ compiler (for the MDsupport and Swilk libraries)
* Numpy ("Numeric") available at http://sourceforge.net/projects/numpy
* Motif discovery programs (AlignACE, Meme, MDscan, etc...) [Installation instructions below]

If you have all these things already installed, you're ready to install TAMO.

****************************************************
***                                              ***
*** Step 1:  setup.py                            ***
***                                              ***
****************************************************

"cd" in to the distribution directory (where this README file resides), and type: 

python setup.py install

After compiling and installing the base package, the script will ask you enter a
path to store data that TAMO will download from the web (e.g. SGD, Whitehead 
Institute ChIP-chip, Human sequence, etc...).  This can be any directory in
which TAMO users have read permission and the installer has write permission.

**********************************************
***                                        ***
***      Step 2: $TAMO variable            ***
***                                        ***
**********************************************

Set a "TAMO" environmental variable equal to TAMOroot in the
TAMO/paths.py file.  THIS STEP IS OPTIONAL, but will be useful when
invoking TAMO command-line utilities.  For example, after you've set
up TAMO, you'll be able to simply invoke "$TAMO/Sitemap.py" in order
to build a motif map from a fasta-formatted file with occurences of
your favorite motif or "$TAMO/AlignAce.py" to run the multi-pass
AlignACE wrapper program.

If your shell is a csh/tcsh derivative, the variable is set executing the line:

   setenv TAMO "/<path-to-TAMOroot/"

and by also putting a line with this command into your .cshrc or .tcshrc.

For sh/bash shells, type
   
   TAMO="/<path-to-TAMOroot/"
   export TAMO

You'll also need to put these lines into your .bashrc file.

***************************************************
***                                             ***
***   Step 3: Install support programs          ***
***                                             ***
***************************************************

TAMO supplies interfaces to AlignACE, MDscan, and Meme.  After these
programs installed, manually set the locations of these programs by
editing $TAMO/paths.py.

Download and build information for each MD program is included here and in
$TAMO/paths.py.

AlignACE can be downloaded after a click-through licence agreement at
the http://atlas.med.harvard.edu/download/.  NOTE: It _does_ work to
download the "linux" AlignACE package and compile under cygwin on 
windows machines.

MEME can be downloaded from http://meme.sdsc.edu/meme/website/meme-download.html.
NOTE: It _does_ work to build MEME under cygwin.

MDscan is available only for linux (as far as I know) after faxing a
licence agreement to the Brutlag Group.  Instructions are at:
http://motif.stanford.edu/distributions/

*** Other Supporing Programs: ROC AUC and WebLogo ***

You may want to install the ROC AUC and MNCP metrics described by
Clarke and Granek, Bioinformatics 2003.  These routines may be
downloaded from the authors' website.  The GetDataFiles.py program can
also be used:

   {full path to TAMO}/TAMO/GetDataFiles.py --Clarke

Finally, the Motif.giflogo() method is an interface to the WebLogo package,
which is available from http://weblogo.berkeley.edu.  If you want
this functionality, you'll need to install the package manually after
running:

   {full path to TAMO}/TAMO/GetDataFiles.py --weblogo

*****************************
***                       ***
***     Documentation     ***
***                       ***
*****************************

Documentation for TAMO modules and routines is available at the TAMO
website (http://jura.wi.mit.edu/fraenkel/TAMO) and is embedded in the
python source code.  For many of the executable programs, instructions
on usage are displayed by invoking the program without arguments.

Documentation can also be accessed from python:

% python
>>> from TAMO import HT
>>> help(HT)

Documentation is not yet redundant throught the source code.  If the
function doesn't have help associated with it, check the module, or,
if appropriate, the object of which the function is a member.