MEME Suite 4.9.0 Patches
This file gives notes and installation instructions for patches of
the MEME Suite version 4.9.0. 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
Contact meme@nbcr.net
if you run into problems.
Patch 1
Download
This patch fixes the following:
- Users of the Google Chrome browser could not submit jobs to MEME-ChIP
because Chrome's validation of number type inputs by default only allow
integers. This has been fixed by specifying the 'any' option for the step
field and by turning off Chrome's automatic validation.
- The server-side validation on MEME-ChIP's page was broken for some
fields.
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@nbcr.net
if you run into problems.
Patch 2
Download
This patch fixes the following:
- Added a citation for CentriMo to the main citation page.
- Uppercased the $home environment variable to $HOME in the installation
documentation. The original $home was for the default for c shell which is now very
uncommon and the more common Bash uses $HOME instead.
- Fixed a bug in the CentriMo graphing code which could cause an infinite loop
and lock up the webpage.
- Changed the description of the
-url option in the iupac2meme
documentation.
- Fixed the fasta-get-markov usage line by removing a incorrect parameter.
- Changed the quick install guide to mention running
make,
make test, make install.
- Improved error reporting for binomial calculations.
- Fixed an incorrect check that was causing GLAM2 to print a warning about
failing to create HTML output when nothing was wrong.
- Changed access of external programs and resources from MEME and GLAM2 to
check the environment variables $MEME_BIN_DIR and $MEME_ETC_DIR before
resorting to the configured default.
- Fixed motif reading code that was rejecting E-values of "0.00e+00".
- Fixed broken link to sample FIMO text file.
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 install the changes from the source directory to the installed version of the
MEME Suite.
Contact meme@nbcr.net
if you run into problems.
Patch 3
Download
This patch fixes the following:
- Appended program name to webservice usage descriptions to make them
easier to search using the Opal interface.
- Fixed mast2text so it can load really big numbers from the residue_count
attribute in the XML.
- Changed a warning message about extremely large description fields of
FASTA sequences to only display once per program invocation.
- Fixed the check of multi-byte characters so it doesn't reject all
non-ASCII characters.
- Fixed the escaping of characters for XML output so it removes characters
that can't be included in XML 1.0 (this is mostly control characters).
- Fixed the ability to select the first sequence database on the CGI pages
for MAST, GOMO, GLAM2SCAN, FIMO and MCAST. It would previously report that
no database was selected when the first sequence database was selected.
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 install the changes from the source directory to the
installed version of the MEME Suite.
Contact meme@nbcr.net
if you run into problems.
Patch 4
Download
This patch fixes the following:
- Changed web-service names to be uppercase without punctuation.
- Fixed MEME's calculation of motif regular expressions (thanks to CSIRO
IT Support for pointing out the problem and attempting to providing a fix)
and updated the broken smoke tests.
- Fixed usage plots.
- Removed month from log file names.
- Added a default pseudo-count of 0.1 to background files generated by
fasta-get-markov to avoid probabilities of zero in higher order
backgrounds.
- Added checks to ensure that background models can't have states with a
probability of zero.
- Updated the licensing links to point to the up-to-date license file.
- Rearranged and simplified CentriMo's result sorting controls.
- Implemented alternative discriminative search mode for CentriMo which
runs in an acceptable time for the web-service but also gives more intuitive
results.
- Added checks to the JSON writing code for the UTF-8 literals U+2028 and
U+2029 which are apparently invalid in Javascript. They should now be encoded
with the correct escape sequence to work in Javascript.
- Fixed DREME's calculation of motifs when the '-norc' option was set.
- Added '-local' option to MEME-ChIP to run CentriMo in local search
mode.
- Fixed a buffer overflow in some MCAST code for pre-processing motifs.
- Fixed a buffer overflow in sequence loading code.
- Added '--parse-genomic-coord' option to FIMO to allow selectively parsing
sequence names. Previously FIMO would always try to parse out genomic
coordinates out of a sequence name which could result in nonsensical
output.
- Changed CentriMo's default thresholding to be more sensible with very few
motifs.
- Updated taipale2meme script to allow conversion of their newest motifs to
MEME motif format.
- Added control to CentriMo output which allows suppression of the
comparative plot.
- Fixed the URL to the header image for GOMO output.
- Updated chen2meme script to support another motif variant.
- Updated downloads link to point to EBI server.
- Changed MEME's system for loading background files to avoid allocating
really large arrays on the stack as this seems to occasionally cause
problems.
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:
This will compile and install the changes from the source directory to the
installed version of the MEME Suite.
Contact meme@nbcr.net
if you run into problems.