MEME Suite 4.10.0 Patches

This file gives notes and installation instructions for patches of the MEME Suite version 4.10.0. 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:

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 command patch -p1 -i patch_4.10.0_1 patch -p1 -i patch_4.10.0_2 patch -p1 -i patch_4.10.0_3 patch -p1 -i patch_4.10.0_4
4. If nothing went wrong then install the changes with the command make install

Please refer to the installation instructions included with the distribution in the file doc/install.html.

Contact meme@sdsc.edu if you run into problems.

Patch 1

This patch fixes the following:

• Fixed running meme-chip on a Windows FAT32 file system where hard links are not supported.
• Fixed the launching of sendmail so the "-t" option is specified.
• Fixed a website problem where submitted files would occasionally not be transfered to the working directory.
• Changed the subject line used by job submission emails so it matches the previous version.

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@sdsc.edu if you run into problems.

Patch 2

This patch fixes the following:

• Fixed incorrect path to GLAM2 logo in the job submission emails.
• Increased GOMo shuffling rounds default on website to match the command-line version.
• Tried to avoid webpage caching for the dynamically generated job status page.
• Fixed spelling of word "occurences" so it now has 2 'r's.
• Fixed configure script so optimisation flags actually work. Optimisation is now enabled by default as intended and as it was in 4.9.1.
• Fixed a compilation error when using clang on OS X.
• Fixed configure script so output of hostname command is now truncated to 1 line by piping output to head. This is to prevent errors due to malformed strings in the Makefiles and config.h .
• Fixed missing CSS styles that caused tabs in DREME's output to display incorrectly.
• Fixed the sample output files so they now look to the EBI server for the logo images and functionality.
• Fixed a potential buffer overflow in CentriMo. To trigger the buffer overflow the first motif in the database had to have multiple equally best scoring sites in the first or second sequence. Beyond that point the buffer would grow large enough that the overflow was exceedingly unlikely.

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@sdsc.edu if you run into problems.

Patch 3

This patch fixes the following:

• Fixes a fprintf parameter that was the wrong type (int instead of double) and caused reading of unallocated memory.
• Fixed validation of GLAM2 motifs for the GLAM2Scan submission page.
• Fixes the MemeSAX library so it will now correctly read MEME XML files where the regular expression representation includes a lower case 'x'.
• Fixes meme_xml_to_html so errors found by the MemeSAX library are now reported and the program exits early with a non-zero status.
• Changed meme so failures in HTML generation cause a non-zero program status which can be detected by tests.
• Adds alternate URLs for the cgi-bin URLs and updates the outputs to use them.

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@sdsc.edu if you run into problems.

Patch 4

This patch fixes the following:

• Sequence updater will now create protein background files for protein sequences instead of the previous behaviour of creating DNA background files for everything

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.

Note if you have already used a previous version of the sequence updater you should delete all the protein background files (matching the pattern "*.faa.bfile") it generated and rerun the updater to regenerate the files properly. As long as the associated sequence files remain it will not need to redownload them.

Contact meme@sdsc.edu if you run into problems.