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Installing InformME

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Jordi Abante edited this page Jun 13, 2018 · 3 revisions

First, make sure you have all the required dependencies installed. Then, acquire the source code either by downloading the zip file or by cloning the git repository:

git clone git@github.com:GarrettJenkinson/informME.git

(If you are behind a firewall, you may need to use the https protocol instead of the git protocol:

git config --global url."https://".insteadOf git://

Be sure to also configure your system to use the appropriate proxy settings, e.g. by setting the https_proxy and http_proxy variables.)

By default, you will be cloning the latest development "master" version of informME. However, you can get a specific version (e.g., v0.3.2) by changing to the informME directory and running

git checkout v0.3.2

Once you have the source code for the appropriate version, run

./install.sh

in the informME directory. During the interactive installation process the user will be asked different questions regarding the locations of default directories. Dependencies, such as GMP, MPFR, MPREAL, and Eigen, will be automatically installed during this process if these are not already available, and the C++ MEX code of informME will be compiled.

Note 1: the following environment variables will optionally be defined in a configuration file stored in ~/.informME/informME.config and then will be accessed throughout multiple points in the informME pipeline:

  • REFGENEDIR: directory where the CpGlocationChr#.mat files will be stored

  • BAMDIR: directory where the BAM files are stored

  • SCRATCHDIR: directory where all temporary files will be stored

  • INTERDIR: directory where all intermediate files will be stored

  • FINALDIR: directory where the output BED files will be stored

  • MATLICENSE: path to MATLAB license

Note 2: The previous environment variables can be overwritten through optional arguments when running any part of informME. If these variables are not defined, then the user must pass the corresponding paths as optional arguments.

If you use informME, please cite:

[1] Jenkinson, G., Pujadas, E., Goutsias, J., and Feinberg, A.P. (2017), Potential energy landscapes identify the information-theoretic nature of the epigenome, Nature Genetics, 49: 719-729.

[2] Jenkinson, G., Abante, J., Feinberg, A.P., and Goutsias, J. (2018), An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data, BMC Bioinformatics, 19:87, https://doi.org/10.1186/s12859-018-2086-5.

[3] Jenkinson, G., Abante, J., Koldobskiy, M., Feinberg, A.P., and Goutsias, J. (2019), Ranking genomic features using an information-theoretic measure of epigenetic discordance, BMC Bioinformatics, 20:175, https://doi.org/10.1186/s12859-019-2777-6.

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