Logo Standalones

Page contents:
How to download the standalone executable
Table 1: MotifSuite executables
Build your commandline

This page provides access, installation and execution guidelines for the standalone use of the softwares in MotifSuite.
If you like our software, please use the citing described in the applications webpage:

ProgramCiting
CreateBackgroundModel Publications
MotifSampler Publications
MotifRanking Publications
FuzzyClustering Publications
MotifComparison Publications
MotifLocator Publications


How to download the standalone executable

We provide access to Linux version 2.6 64bit executables, statically linked against libstdc++6 (gcc version 4.1.2). Normally, they should run on any linux distribution. A 32bit executable can be made available on request.

For all applications except FuzzyClustering, the executable is the only software to be installed. For FuzzyClustering, you need to install additional supporting software: 1) MCRInstaller.bin (Matlab_Compiler_Runtime) and 2) libClust.tar.gz (a dynamically linked library).

To start with, define your path on which you will install the executables:
- <SOFTWARE_PATH>: the path on your platform in which you will install the requested executable

ActionExample|Command
Click on the link in table 1 and save the executable (binary file) in <SOFTWARE_PATH>
Go to directory in which your executable was saved~> cd <SOFTWARE_PATH>
Update the executables permissionseg <SOFTWARE_PATH> ~> chmod 755 MotifSampler
For FuzzyClusterng first install MCR and libClust SEE MORE INFO BELOW
Check if it works by calling the application without optionseg <SOFTWARE_PATH> ~> ./MotifSampler

The output should look like this (example for MotifSampler):

Fig fail: MS_input.png


This section only applies to FuzzyClustering:
The FuzzyClustering executable is dynamically linked against an in Matlab created shared library (libClust.so). You do not need an installed Matlab software neither Matlab license. Instead, you have to install a Matlab Compiler Runtime (MCR version 7.8 (32bit) or 7.9 (64bit)) which is freely available and provided in table 1. The MCR (about 600MB) needs to be installed once, re-installation is only needed when a new libClust library would be released that was created with a Matlab version different from the one you have installed (which we would mention here).

Define the path on which you will install MCR and libClust (may be but is not necessarily equal to <SOFTWARE_PATH>):
- <MCRCLUST_PATH>: the path on your platform in which you will install MCR and libClust

ActionExample|Command
Click on the link in table 1 and save the MCR (binary file) in <MCRCLUST_PATH>
Go to directory in which the MCR was saved~> cd <MCRCLUST_PATH>
Launch the installation of the MCR software~> ./MCRInstaller.bin -console
It will ask you for 'Destination directory': change the default into <MCRCLUST_PATH>Matlab_Compiler_Runtime/eg /home/motif_software/Matlab_Compiler_Runtime/
Wait until this process ends Successfully (this may take a while)
Optionally you can remove the MCRInstaller.bin file
(it is 250MB and not needed anymore for further operation)
~> rm -f MCRInstaller.bin
--
Click on the link in table 1 and save libClust.tar.gz (tar file) in <MCRCLUST_PATH>
Go to the directory in which libClust.tar.gz was saved~> cd <MCRCLUST_PATH>
Untar the library into <MCRCLUST_PATH>eg ~> tar -zxvf libClust.tar.gz -C /home/motif_software/
Optionally you can remove the libClust.tar.gz file
(it is not needed anymore for further operation)
~> rm -f libClust.tar.gz
--
Export the library paths to your system environment variable (*)
for 64_bit:
~> setenv LD_LIBRARY_PATH <MCRCLUST_PATH>Matlab_Compiler_Runtime/v79/runtime/glnxa64/:<MCRCLUST_PATH>libClust
eg for 64_bit: ~> export LD_LIBRARY_PATH=/home/motif_software/Matlab_Compiler_Runtime/v79/runtime/glnxa64:/home/motif_software/libClust
--
Go to directory in which FuzzyClustering was saved~> cd <SOFTWARE_PATH>
Verify if the libraries are correctly linked, the output should look like:
libmwmclmcrrt.so => <MCRCLUST_PATH>Matlab_Compiler_Runtime/v79/runtime/glnxa64/libmwmclmcrrt.so (0x00002b441f6a0000)
libClust.so => <MCRCLUST_PATH>libClust/libClust.so (0x00002b441f89f000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002b441fabd000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b441fdbe000)
libm.so.6 => /lib64/libm.so.6 (0x00002b441ffcc000)
libc.so.6 => /lib64/libc.so.6 (0x00002b442024f000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002b44205a6000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b44207aa000)
/lib64/ld-linux-x86-64.so.2 (0x00002b441f682000)
~> ldd FuzzyClustering
If the output reports 'not found', verify your LD_LIBRARY_PATH setting (~> echo LD_LIBRARY_PATH) or contact us.

(*) depending on your platform (bash or shell), you need to use 'export' instead of 'setenv' command.
64_bit: export LD_LIBRARY_PATH=<MCRCLUST_PATH>Matlab_Compiler_Runtime/v79/runtime/glnxa64/:<MCRCLUST_PATH>libClust
You may need to restart your computer (or re-login) to have the environment settings activated.



Table 1: MotifSuite executables

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ProgramDescriptionDownload
CreateBackgroundModelcreates a genome-specific higher-order background model for a set of DNA sequences
MotifSamplera probabilistic de novo motif detection tool designed to search for regulatory motifs in DNA sequences upstream of coregulated genes from one species
MotifRankingprioritizes the different significant motifs from a list of putative motifs in PWM format obtained by running MotifSampler multiple times on the same input DNA sequences set
FuzzyClusteringclusters the different significant motif instances from a list of putative motifs in instances format obtained by running MotifSampler multiple times on the same input DNA sequences set
MotifComparisoncomputes the similarity between each pair of motif PWMs coming from two input files
MotifLocatorprovides genome-wide screening of DNA sequences for instances of a given motif PWM


Build your commandline

The command to run an application consists of the application's name followed by a set of switches that relate to the application arguments. A switch is a one letter symbol preceded by the symbol '-' and is separated from its argument by a space. The arguments can be one of the following:
- required input for the program, if not the application fails to run
- program parameter settings, if not defined the application uses the programs default settings
- outputfile name and path in which the results must be written to, if not the output is only printed to the screen (STDOUT). If you only supply an outputfile name without path, the file will be stored in <SOFTWARE_PATH> (assuming you call the application from <SOFTWARE_PATH>)

Command example: <SOFTWARE_PATH> ~> ./MotifSampler -f demo.fna -b athaliana_3.bg -s 1 -w 8 -p f0_1 -n 3 -r 100 -o demo.gff -m demo.mtrx
Mark that we advise to call the application from <SOFTWARE_PATH> and that the application's name is preceded by the './' prefix. This is to assure that you actually run the version of MotifSampler that you view and that you don't run earlier releases of MotifSampler installed somewhere else on your platform.

For each application, the list of switches and definition of its related argument as also program default settings can be uploaded from the executable with the help command (<SOFTWARE_PATH> ~> ./MotifSampler -h). However, we strongly recommend the MotifSuite webpages for a more comprehensive description of all switches and arguments.
Please read more:

                                      
Programlink to webpagelink to guidelines
CreateBackgroundModelargumentsguidelines
MotifSamplerargumentsguidelines
MotifRankingargumentsguidelines
FuzzyClusteringargumentsguidelines
MotifComparisonargumentsguidelines
MotifLocatorargumentsguidelines


Feedback

Contact us if you have comments, questions or suggestions or simply want to react on the contents of this guideline. Thank you.