MEME Suite 4.10.1 Patches
This file gives notes and installation instructions for patches of
the MEME Suite version 4.10.1. For new
installations you can skip the patching steps by using the
pre-patched distribution.
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
Please refer to the installation instructions included with the distribution
in the file doc/install.html.
Contact meme-suite@uw.edu
if you run into problems.
Patch 1
Download
This patch fixes the following:
- Changed GenbankUpdater to trim the name of the listing to handle cases where files had leading underscores.
- Changed sort of sequence databases to be case insensitive and to ignore leading spaces.
- Changed sequence database overview page to load information on demand. This should make it more responsive.
- Made disallowed alphabets for sequence inputs more obvious by using a red cross-out over the names.
- Fixed inclusion of example files for GLAM2 and minimal MEME motifs for the website install.
- Fixed a server error caused by the absence of cookies.
- Fixed submission to Tomtom from GLAM2 DNA output.
- Fixed format specifier used to write out unusual Unicode characters to JSON format.
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.
Contact meme-suite@uw.edu
if you run into problems.
Patch 2
Download
This patch fixes the following:
- Inconsistent results with GLAM2 on different architectures. Note:
This change uses a new random number generator so new results with GLAM2
will differ slightly from old results.
- Failure to produce sequence logos for GLAM2 motifs with pure
deletion columns.
- AME bug causing the maximum motif width to be incorrect causing a
dependency on motif order.
- AME bug causing crash (segment fault).
- Failure to log AME jobs.
- Fixed mangling of non-ASCII form input to all MEME Suite web server forms.
- Fixed error message when there are no installed sequence databases.
- Cleaned up GOMo documentation.
- Cleaned up Alternate Servers section of website menu.
- Improved update-plot-usage script.
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:
Trouble-shooting: This patch requires automake
version 1.14. If you have trouble installing this patch, we recommend you install the
pre-patched distribution instead.
Now run:
This will copy the change from the source directory to the installed version of the
MEME Suite.
Contact meme-suite@uw.edu
if you run into problems.
Patch 3
Download
This patch fixes the following:
- Changed download page to prevent caching of the inner frame in the Safari web browser.
- Changed motif input to display the motifs under categories.
- Changed the motif database system to support subfolders.
- Improved the error message the MEME reports when given a single sequence without using "any number of repeats" (ANR) mode.
- Fixed incorrect URL in RSAT downloader configuration. Server operators should delete the existing
RsatUpdater.properties configuration file under DB_DIR/fasta_databases/conf/ so it can be recreated.
- Added logic to categorize RSAT upstream sequence databases by taxon to make them easier to find. Server operators should consider removing the existing RSAT databases so the old "Upstream Databases" category is not displayed.
- Changed the motif and sequence database overview pages to display the database count for each category.
- Added links for viewing the load on the alternative servers.
- Added a rate limiter to the job status page so the automated refresh feature doesn't put unnecessary load on the server.
- Updated the MEME-ChIP documentation to cover some missing flags.
- Fixed a bug in the website FASTA file validator which was incorrectly rejecting sequence weights for being out of range.
- Tweaked the options to the sequence database downloader so it is easier to run only a single updater.
- Added more obvious links to the motif database overview page from the job submission pages.
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.
Contact meme-suite@uw.edu
if you run into problems.
Patch 4
Download
This patch fixes the following:
- Fixed the update-sequence-db program to actually delete obsolete
databases when using the "--delete_old" option.
- Added a new option "--obsolete <file pattern>" to
update-sequence-db to allow a server administrator to manually mark
sequence databases as obsolete.
- Added documentation on the database schema used by update-sequence-db.
- Changed the webserver FASTA file validator/standardizer to read the
weights as BigDecimal which allows them to be written out with identical
precision. This avoids a bug where small but non-zero weights would be
written out as zero.
- Added additional check to all job submission forms to ensure the
combined form input size is smaller than 80MB.
- Fixed a bug where the webserver was not logging the job submission times.
- Added a per-user quota to avoid single users filling up the entire
server queue for hours. By default this quota is unbounded but it can be
changed by editing the file
MemeSuite.properties.
- Fixed the parsing of MEME motif files to handle cases when the
E-values are written out in different formats.
- Fixed the writing of MEME motif files so the E-values are written out
using the same formatting in (hopefully) all circumstances.
- Fixed the logic used to display server news and notices to take into
account differences between the clock of the server and the local
computer's clock.
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.
Contact meme-suite@uw.edu
if you run into problems.