MEME Suite 4.9.1 Patches
This file gives notes and installation instructions for patches of
the MEME Suite version 4.9.1. For new
installations you can skip the patching steps by using the
pre-patched distribution.
You need to install up to patch 2 to enable Opal 2.5 support.
The patches should always be installed in order because
later patches may depend on changes made in earlier patches.
If you're patching a completely unpatched MEME install then all the
patches can be installed by:
- Downloading all the patch files (linked above) to the root of the
MEME Suite source distribution
- Changing your working directory to the root of the MEME Suite source distribution
- Running the command
- If nothing went wrong then install the changes with the command
Contact meme@sdsc.edu
if you run into problems.
Patch 1
Download
This patch fixes the following:
- Fixed a call to seek in the meme-chip script where the position and
constant were reversed. This was not causing problems because both had
the value zero.
- Increased the column span of the detailed information box for MCAST
so it can span the page like it was meant to.
- Fixed typos describing MCAST as MAST in the results help
information.
- Fixed a problem with the motif parser where whitespace after the
alphabet string in text format motifs would not be trimmed. This was
resulting in odd errors complaining the alphabet was wrong.
- Fixed a warning message caused by attempting to print an undefined
variable in MEME ChIP output.
- Improved the warning messages generated by Perl library JsonWr.
- Fixed a bug in the HTML parsing code with a rare trigger. The last two
characters of a self-closing tag (eg. <br/>) had to be split over 2
reads.
- Fixed Tomtom so it doesn't crash when there are no target motifs in
the provided files. It now provides a warning when any target motif files
are empty.
- Added a timeout to all the MEME Suite services that didn't already
have one.
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 compile and reinstall the updated MEME Suite.
Contact meme@sdsc.edu
if you run into problems.
Patch 2
Download
This patch fixes the following:
- Fixed the fasta-fetch script so that the output actually goes to the
file specified and not partly to standard output. Thanks to
Leighton Pritchard for submitting this fix.
- Changed the encoding of sequence descriptions when they are sent to
the Opal webservice. This is to correct some incompatibilities found with
the previously used URL encoding.
- Fixed the parsing of decimal values with more than 20 characters.
The parser was previously returning zero for such values.
- Fixed the parsing of text motifs with only score matricies. Previously
the parser would return a broken probability matrix, sometimes containing
NaN values because the site count would be set to zero. Now when the site
count is unset it defaults to 100 for the purpose of conversion.
- Fixed a warning in the MAST webservice for an undefined variable
access.
- Updated Tomtom to only use the number of motif sites when it is
actually set.
- Updated the Makefile to make deployment to Opal 2.5 possible without
fiddly manual copying and renaming of files. This overloads the
--enable-webservice configure option so if a file is specified it assumes
it is the Opal 2.4 build.xml but otherwise it assumes that the value is the
absolute path to the Opal 2.5 deploy directory.
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:
Note: if you are installing this to work with Opal 2.5 you will need to
set the value of the --enable-webservice configure option to point at the
Opal 2.5 deploy directory NOT the Opal build.xml. For example:
Now run:
This will compile and reinstall the updated MEME Suite.
Contact meme@sdsc.edu
if you run into problems.