MUMMIE Downloads

The current version of the software is: 0.1.

source code (C++/Perl)
linux binaries (requires shared objects: see below)
virtual machine (requires Oracle VirtualBox)
microMUMMIE: microRNA target prediction using MUMMIE (programs / inputs)

Note: MUMMIE compiles on Linux 3.1.0-7.fc16i686 / gcc 4.6.2 (Red Hat 4.6.2-1) SMP. Statically-linked binaries are not available at this time due to difficulty obtaining static archive files for several libraries. We hope to resolve this issue shortly. Meanwhile, the software runs fine with shared libraries (see below). Also, you can now install a virtual machine that has MUMMIE already installed within it. Click on the link above.

Instructions:

1. Download files into a new directory ("BASE")

2. Unpack the archives via the commands:

tar xvfz
mummie.tgz

tar xvfz linux.tgz

3. Set your PATH directory list to include BASE, BASE/MUMMIE, and BASE/perl

4. Set your PERLLIB directory list to include BASE/perl

5. Change file permissions via the command:

chmod a+x */*.pl
*/*/*.pl

6. Ask your system administrator to install the following packages: gsl, gsl-devel, mpi, mpi-devel, gcc, gcc-c++. If you do not have a system administrator, you can install these packages by logging in as root (command: su - root) and using the yum or apt-get program, e.g., yum install gsl-devel, etc.

7. Edit the file BOOM/makefile; change the

CFLAGS
-I

setting to the directory where mpi.h is located (usually under /usr/lib/... or /usr/include...)

8. Compile the source code, via the command:

cd src/MUMMIE ;
make

9. Check that the compile succeeded by running core MUMMIE programs (in the src/MUMMIE directory) such as parse, baum-welch, and hmm-edit

10. [OPTIONAL] For miRNA target-site prediction, the program microMUMMIE.pl provides a template for a basic target prediction pipeline, which you will need to modify as per your particular requirements. You will need to install PARalyzer and run it to obtain the distributions.csv file; also, to use conservation evidence you will need to obtain alignments of your target sequences and run a conservation tool such as the branch-length-score program in the TargetScan package by Bartel et al. Please see the microMUMMIE page for details.

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