The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS). MethPipe provides tools methylation-specific technical evaluation of sequencing data, and for estimating methylation levels at individual cytosines. Additionally, MethPipe includes tools for identifying higher-level methylation features, such as hypo-methylated regions (HMR), partially methylated domains (PMD), hyper-methylated regions (HyperMR), and allele-specific methylated regions (AMR).

This release may be unstable. Much has changed in 4.0.0 compared with earlier releases. The main new functionality is the capacity for reading most (large) input files in gzip format. Installing version 4.0.0 may be less convenient. It requires building and installing the smithlab_cpp library first. The instructions for installing earlier releases are below.

• The GNU Scientific Library: this has always been required. It can be installed using apt on Linux, using brew on macOS, or from source available here.
• The Zlib compression library. Most likely you already have this installed on your system. If not, it can be installed using apt on Linux through the package zlib1g-dev. On macOS, Zlib can be installed with brew.
• The smithlab_cpp library. We suggest you install a release, and do not attempt to simply clone the source and build the library unless you know what you are doing. Currently the best way to install the smithlab_cpp library is using ./configure && make && make install but please see the instructions here
• Optional: The HTSlib library, which can be installed through brew on macOS, through apt on Linux, or from source downloadable here. This is only required for using the to-mr tool, but it you plan to build methpipe with HTSlib support, then make sure you also build smithlab_cpp with HTSlib support.

1. Download methpipe-4.0.0.tar.gz here.
2. Unpack the archive:

$ tar -zxvf methpipe-4.0.0.tar.gz

3. Move into the methpipe directory and create a build directory:

$ cd methpipe-4.0.0
$ mkdir build
$ cd build

4. Run the configuration script:

$ ../configure

If you do not want to install the methpipe system-wide, or if you do not have admin privileges, specify a prefix directory:

$ ../configure --prefix=/some/reasonable/place

If you are specifying a particular location for installing methpipe then you likely did the same thing when installing smithlab_cpp. If so, you must configure as follows:

$ ../configure --prefix=/some/reasonable/place \
    CPPFLAGS='-I /path/to/smithlab_cpp/headers' \
    LDFLAGS='-L/path/to/smithlab_cpp/lib'

Notice that the argment to LDFLAGS does not have a space after the -L. This next argument is not required, but will make the code run slightly faster:

$ ../configure CXXFLAGS='-O3 -Wall'

Finally, if you want to build with HTSlib support (for the to-mr program) then you need to specify the following:

$ ../configure --enable-hts

And if you installed HTSlib yourself in some non-standard directory, you must specify the location like this:

$ ../configure --enable-hts CPPFLAGS='-I /path/to/htslib/headers' \
    LDFLAGS='-L/path/to/htslib/lib'

If you need to specify locations for both HTSlib and smithlab_cpp, then they must be in the same sets of quotes, separated by spaces. Hopefully this process will be easier soon.

If you are still in the build directory, run make to compile the tools, and then make install to install them. If your HTSlib is not installed system-wide, then you might need to udpate your library path:

$ export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/path/to/htslib/lib

You may download the latest stable release from http://smithlabresearch.org/software/methpipe/ This software package has been designed to operate in a UNIX-like environment. It has been tested on MacOS X Snow Leopard and Linux.

• Step 0

  This software package requires a functioning installation of the GNU Scientific Library (GSL). If you don't already have this installed, you will need to download and install it from http://www.gnu.org/software/gsl/

  If gsl is not installed in the default path,

  export CPATH=/path_to_my_gsl/include
  export LIBRARY_PATH=/path_to_my_gsl/lib
  

  will add search paths for compiling and linking.

• Step 1

  To build the binaries, type the following, where '>' is your prompt and the CWD is the root of the distribution:

  > make all
  

• Step 2

  To install the binaries, type the following, where '>' is your prompt and the CWD is the root of the distribution:

  > make install
  

  This will place the binaries in the bin directory under the package root. They can be used directly from there without any additional steps. You can add that directory to your PATH environment variable to avoid having to specify their full paths, or you can copy the binaries to another directory of your choice in your PATH

For advanced users who are interested in the newest features, you may obtain the latest source code by cloning the MethPipe repository:

> git clone --recursive https://github.com/smithlabcode/methpipe.git

After you clone the latest source code, follow the above steps for installation.

Read methpipe-manual.pdf in the docs directory.

Andrew D. Smith [email protected]

Ben Decato [email protected]

Meng Zhou [email protected]

MethPipe and MethBase Users' Mailinglist [email protected] http://groups.google.com/group/methpipe

Copyright (C) 2018-2020 University of Southern California, Andrew D. Smith

Current Authors: Andrew D. Smith, Ben Decato, Meng Zhou, Liz Ji, Jenny Qu, Egor Dolzhenko

This is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.