diff -r 166f68c0b089 doc/ame.html --- a/doc/ame.html Fri Apr 07 18:02:37 2017 -0700 +++ b/doc/ame.html Sat May 20 17:54:43 2017 -0700 @@ -200,6 +200,7 @@ Markov Background Model format as the background model for converting the position-specific probability matrix (PSPM) motifs into position-specific log-odds scoring matrices (PSSM). + The background model normalizes for biased distribution of single letters in the sequences. This option overrides the --bgformat option. Use frequencies based on the motif file or files. See also --bgformat diff -r 166f68c0b089 doc/development/meme_suite_proj_overview.html --- a/doc/development/meme_suite_proj_overview.html Fri Apr 07 18:02:37 2017 -0700 +++ b/doc/development/meme_suite_proj_overview.html Sat May 20 17:54:43 2017 -0700 @@ -1,64 +1,125 @@ - - - - + MEME Suite Project Overview + -

MEME Suite Project Overview

- - - + + +

MEME Suite Overview

+The MEME Suite project is a collection of command line tools for motif analsyis, +and a web site that allows users to run the main MEME Suite tools via a web interface. +We maintain two publicly available instances of the web site: +
http://meme-suite.org, +hosted in the Amazon EC2 cloud, +and +http://alternate.meme-suite.org, +hosted in the Google Compute Engine cloud. +

+Users may download the source for the MEME Suite from either web site. +Generally users will only want to build the command line tools. +We discourage inexperienced users from trying to build the web site. +They're welcome to try, +but we don't have the resources to teach basic web server adminstration. +

+The MEME Suite is implemented using multiple languages. +The primary tools are written in C, +supplemented by scripts in Perl and Python. +The output of the MEME Suite programs includes HTML with embedded JavaScript. +The web applications are implemented as Java Servlets running under +Apache Tomcat. + +

Source Code Repository and Organization

+The source code repository for the MEME Suite is hosted on Bitbucket +at https://bitbucket.org/tlbailey/meme. +To be added to the project create a +BitBucket +account, and send your BitBucket user name to +Charles Grant, +Tim Bailey, +or +Bill Noble. +

+The project is organized in multiple directories: +

+
doc
+
Documentation for end users and developers. +Mostly HTML supplemented by CSS, images, and JavaScript. +This directory also contains the sample output for the MEME Suite tools.
+
etc
+
Data files and output templates used at run time by the MEME Suite +programs.
+
scripts
+
Perl and Python scripts
+
src
+
C source code
+
tests
+
Scripts and data for integration (smoke) tests
+
website
+
Java, JavaScript, CSS, and output templates, used by the web applications.
+
+ +

Building the MEME Suite

+The MEME Suite uses the +
autools +to automate building the MEME Suite from source. +Most MEME Suite users will be building on Linux or OS X. +We don't support building the MEME Suite directly on Windows, +but it can be built using Cygin on Windows or in the Windows 10 Ubuntu +subsystem. +

+The steps for building the MEME Suite: +

    +
  1. Check out a working copy of the source code from the repository
  2. +
  3. cd into the root of the working repository
  4. +
  5. Run ./bootstrap (this step is only needed for the first build in a working copy)
  6. +
  7. Run ./configure +The configure command accepts multiple options. +These are documented in the +user installation guide. +
  8. +
  9. Run make
  10. +
  11. Run make test
  12. +
  13. Run make install
  14. +
diff -r 166f68c0b089 doc/download-index.html --- a/doc/download-index.html Fri Apr 07 18:02:37 2017 -0700 +++ b/doc/download-index.html Sat May 20 17:54:43 2017 -0700 @@ -109,11 +109,13 @@ Patches - 4.11.4Apr 06 2017 - - + 4.11.4Apr 06 2017May 18 2017 + Readme + meme_4.11.4_1.tar.gz meme_4.11.4.tar.gz +