MEME Suite 4.8.1 Patches

This file gives notes and installation instructions for patches of the MEME Suite version 4.8.1.

The patches should always be installed in order because later patches may depend on changes made in earlier patches.

If you're patching a fresh MEME install then all the patches can be installed by:

1. Downloading all the patch files (linked above) to the root of the MEME Suite source distribution
2. Changing your working directory to the root of the MEME Suite source distribution
3. Running the commands patch -p0 -i patch_4.8.1_1 patch -p1 -i patch_4.8.1_2 patch -p1 -i patch_4.8.1_3 patch -p0 -i patch_4.8.1_4 patch -p1 -i patch_4.8.1_5
4. If nothing went wrong then install the changes with the command make install

Contact meme@nbcr.net if you run into problems.

Patch 1

It is only necessary to apply this patch if you are running a copy of the MEME Suite Web services or if you need to install later patches.

This patch fixes the following:

• The MotifUtils.pm module had a bug where it used the alphabet size in place of the motif width when applying pseudocounts to a count matrix. This meant that rows after the 4th did not get pseudocounts applied.

To apply this patch, download the patch file to the root of the MEME Suite source distribution, change your working directory to the root of the MEME Suite source distribution and run the command:

You should see the following message:

Now run:

This will copy the change from the source directory to the installed version of the MEME Suite web server.

Contact meme@nbcr.net if you run into problems.

Patch 2

This patch fixes the following:

• For long sequences the combined block diagram in MEME text output could be longer than the buffer allowed for parsing it. This patch makes the block diagrams line wrap.
• The MEME motif parsing code was updated to handle the line wrapped block diagrams.
• The line wrapping fix also caused most of the MEME tests to break. The tests have been updated.
• A MAST bug effecting the background frequencies used for scanning protein sequences or DNA sequences with protein motifs was discovered and fixed. Unfortunately this bug has been present since MEME 4.6.0.
• MAST's calculation of motif correlation used to include scoring columns of ambiguous letters. It has been updated to only check the correlation of non-ambiguous columns.
• Updated MEME Suite programs to check an environment variable for the location of the etc directory (this helps with testing before installation).
• The SpaMo output folders had been accidentally left out of the downloadable results for MEME-ChIP.
• Fixed nmica2meme script so it can handle a singular motif. Made the <motifset> outermost tag optional for a single motif.
• Fixed a bug in GLAM2 CGI where it was incorrectly reading the value of the initial aligned columns.
• Fixed a bug in the MEME web service script where it was passing an incorrect argument to psp-gen for protein sequences.

To apply this patch, first apply previous patches. Then download the patch file to the root of the MEME Suite source distribution, change your working directory to the root of the MEME Suite source distribution and run the command:

You should see the following messages:

If everything worked then run:

Which will compile and install the changes.

Contact meme@nbcr.net if you run into problems.

Patch 3

This patch fixes the following:

• Fixed "-update" flag for metatest when source is standard out.
• Fixed most MEME memory issues reported by valgrind.
• Removed instances of the keyword "extern" where it was used incorrectly.
• Removed the text saying "New" on the website for the MEME discriminative sequence input.
• Replaced all document.write calls in CentriMo output to work around a Firefox bug where parts of the page written with a document.write call are saved when "Web Page, complete" is used as the saving option. See https://bugzilla.mozilla.org/show_bug.cgi?id=118792 for Firefox bug.
• Fixed a bug in DREME's code for checking the ghostscript version. It used to accept any version less than 9.x where x was larger than 15 however the intent was to only accept versions larger than 8.15.
• Fixed a bug with higher order background models which affected gendb and ama.
• Changed CentriMo so flipping is not enabled by default. It was decided that this was confusing the results.
• Added "-flip" flag to CentriMo test so the result file does not need updating.
• Changed CentriMo output to display the total sites column by default.
• Fixed an oddity in the MEME HTML output where in some places it was counting the start of a sequence as zero and in other places it was counting the start of a sequence as 1. Now all should count from 1 in the HTML output.
• Fixed psp-gen so it handles ambigious characters and updated the associated documentation.
• Fixed FIMO documentation on the p-value and q-value thresholds.
• Fixed CentriMo's broken command-line option "-motif".
• Fixed divide by zero error in CentriMo in the unusual case where the total sites for a motif are zero.
• Fixed display of zeros in the CentriMo results.
• Fixed the CentriMo webservice so the maximum central window option uses the correct argument when calling centrimo.
• Fixed a bug in the motif parsing code where the final motif would not be returned when a MEME text format file of exactly the right size would cause the final read to be of size zero.
• Improved the error message given by ceqlogo when no motifs are loaded.

To apply this patch, first apply previous patches. Then download the patch file to the root of the MEME Suite source distribution, change your working directory to the root of the MEME Suite source distribution and run the command:

You should see the following messages:

If everything worked then run:

Which will compile and install the changes.

Contact meme@nbcr.net if you run into problems.

Patch 4

It is only necessary to apply this patch if you are running a copy of the MEME Suite Web services or you need to install later patches. It fixes errors in the psp-gen documentation and the MEME web services.

To apply this patch, download the patch file to the root of the MEME Suite source distribution, change your working directory to the root of the MEME Suite source distribution and run the command:

You should see the following messages:

Now run the command:

This will copy the changes from the source directory to the installed version of the MEME Suite web server.

Contact meme@nbcr.net if you run into problems.

Patch 5

This patch updates external links. Specifically it adds the EBI alternate server and removes the QBI alternate server. It also updates the forum links and adds the new google group link.

To apply this patch, download the patch file to the root of the MEME Suite source distribution, change your working directory to the root of the MEME Suite source distribution and run the command:

You should see the following messages:

Now run the commands:

This will copy the changes from the source directory to the installed version of the MEME Suite web server.

Contact meme@nbcr.net if you run into problems.