diff --git a/README.md b/README.md index e3ffe8d..35520e0 100644 --- a/README.md +++ b/README.md @@ -1,58 +1,159 @@ The MethPipe software package is a computational pipeline for -analyzing bisulfite sequencing data (WGBS and RRBS). MethPipe -provides tools for mapping bisulfite sequencing read and estimating -methylation levels at individual cytosine sites. Additionally, -MethPipe also 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). - -Building and Installing -======================= - -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. +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). + +Major release 4.0.0 +=================== + +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. + +## Installing release 4.0.0 + +### Required libraries + +* 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](http://www.gnu.org/software/gsl). +* 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](https://github.com/smithlabcode/smithlab_cpp) +* Optional: The HTSlib library, which can be installed through `brew` + on macOS, through `apt` on Linux, or from source downloadable + [here](https://github.com/samtools/htslib). 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. + +### Configuration + +1. Dowload methpipe-4.0.0.tar.gz [here](https://github.com/smithlabcode/methpipe). +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. + +### Building and installing the tools + +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 +``` + +Previous releases of Methpipe +============================= + +Building and Installing +----------------------- + +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, + 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. + 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 + 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: + of your choice in your PATH - > git clone --recursive https://github.com/smithlabcode/methpipe.git - -After you clone the latest source code, follow the above steps for installation. +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. Usage ===== @@ -68,9 +169,12 @@ andrewds@usc.edu Ben Decato decato@usc.edu +Meng Zhou +mengzhou@usc.edu + MethPipe and MethBase Users' Mailinglist methpipe@googlegroups.com -http://groups.google.com/group/methpipe?hl=en +http://groups.google.com/group/methpipe Copyright and License Information ================================= @@ -78,23 +182,15 @@ Copyright and License Information 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 program 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 program 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. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - -SamTools -Copyright (c) 2008-2009 Genome Research Ltd. -SamTools software is free software distributed under the MIT License. -Refer to the COPYING file in src/samtoos/ for further information. + +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.