README.md: updates for installing v1.5.0

Author: andrewdavidsmith

README.md

@@ -6,228 +6,106 @@
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 DNMTools is a set of tools for analyzing DNA methylation data from
-high-throughput sequencing experiments, especially whole genome
-bisulfite sequencing (WGBS), but also reduced representation bisulfite
-sequencing (RRBS). These tools focus on overcoming the computing
-challenges imposed by the scale of genome-wide DNA methylation data,
-which is usually the early parts of data analysis.
+high-throughput sequencing experiments, especially whole genome bisulfite
+sequencing (WGBS), but also reduced representation bisulfite sequencing
+(RRBS). These tools focus on overcoming the computing challenges imposed by
+the scale of genome-wide DNA methylation data, which is usually the early
+parts of data analysis.
 
-## Installing release 1.4.4
-
-The documentation for DNMTools can be found
-[here](https://dnmtools.readthedocs.io). But if you want to install
-from source and you are reading this on GitHub or in a source tree you
-unpacked, then keep reading. And if you are in a terminal, sorry for
-all the formatting.
-
-### Required libraries
-
-* A recent compiler. Most users will be building and installing this
-  software with GCC. We require a compiler that fully supports C++17,
-  so we recommend using at least GCC 9 (released in 2019). There are
-  still many systems that install a very old version of GCC by
-  default, so if you have problems with building this software, that
-  might be the first thing to check. The clang LLVM compiler can
-  also be used with a recent enough version.
-* The GNU Scientific Library. It can be installed using apt on Linux
-  (Ubuntu, Debian), using brew on macOS, or from source available
-  [here](http://www.gnu.org/software/gsl).
-* The HTSlib library. This can be installed through brew on macOS,
-  through apt on Linux (Ubuntu, Debian), or from source downloadable
-  [here](https://github.com/samtools/htslib).
-
-All the above can also be installed using conda. If you use conda for
-these dependencies, even if you are building dnmtools from the source
-repo, it is easiest if all dependencies are available through conda.
-
-### Configuration
-
-* Download [dnmtools-1.4.4.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.4.4/dnmtools-1.4.4.tar.gz).
-* Unpack the archive:
-```console
-tar -zxvf dnmtools-1.4.4.tar.gz
-```
-* Move into the dnmtools directory and create a build directory:
-```console
-cd dnmtools-1.4.4 && mkdir build && cd build
-```
-* Run the configuration script:
-```console
-../configure
-```
-If you do not want to install DNMTools system-wide, or if you do
-not have admin privileges, specify a prefix directory:
-```console
-../configure --prefix=/some/reasonable/place
-```
-If you installed HTSlib yourself in some non-standard directory,
-you must specify the location like this:
-```console
-../configure CPPFLAGS='-I /path/to/htslib/headers' \
-             LDFLAGS='-L/path/to/htslib/lib'
-```
-Depending on how you obtained HTSlib, the headers may not be
-in a directory at the same depth as the library file.
-
-### 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:
-```console
-make && make install
-```
-If your HTSlib (or some other library) is not installed system-wide,
-then you might need to udpate your library path:
-```console
-export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/path/to/htslib/lib
-```
-
-### Testing the program
-
-To test if everything was successful, simply run `dnmtools` without
-any arguments and you should see the list of available commands:
-```console
-dnmtools
-```
-There is a test suite for `dnmtools` and these test can be performed
-as follows:
-```console
-make check
-```
-This must be done from the build directory. Note that the tests
-performed with `make check` are mostly regression tests that cover
-prior issues rather than coverage tests to test all the functionality
-of `dnmtools`.
-
-### Using a clone of the repo
-
-We strongly recommend using DNMTools through the latest stable release
-under the releases section on GitHub or through a package as with
-conda/mamba.  Developers who wish to work on the latest commits, which
-are unstable, can compile the source using `autogen.sh` which just
-wraps `autoreconf`.
+**Nanopore** As of v1.5.0, DNMTools has funcionality to start analysis with a
+BAM file from Nanopore sequencing with 5mC and 5hmC calls at CpG sites.
 
 ## Usage
 
-Read the [documentation](https://dnmtools.readthedocs.io) for usage of
-individual tools within DNMTools.
-
-## Installing and running `dnmtools` docker images
-
-The docker images of `dnmtools` are accessible through GitHub Container
-registry. These are light-weight (~30 MB) images that let you run `dnmtools`
-without worrying about the dependencies.
-
-### Installation
-
-To pull the image for the latest version, run:
-```console
-docker pull ghcr.io/smithlabcode/dnmtools
-```
-To test the image installation, run:
-```console
-docker run ghcr.io/smithlabcode/dnmtools
-```
-You should see the help page of `dnmtools`.
-
-For simpler reference, you can
-re-tag the installed image as follows, but note that you would have to re-tag
-the image whenever you pull an image for a new version.
-```console
-docker tag ghcr.io/smithlabcode/dnmtools:latest dnmtools:latest
-```
-
-You can also install the image for a particular vertion by running
-```console
-docker pull ghcr.io/smithlabcode/dnmtools:v[VERSION NUMBER] #(e.g. v1.4.4)
-```
-Not all versions have corresponding images; you can find available images
-[here](https://github.com/smithlabcode/dnmtools/pkgs/container/dnmtools).
-
-### Running the docker image
-
-To run the image, you can run (assuming you tagged the image as above)
-```console
-docker run -v /path/to/data:/data -w /data \
-  dnmtools [DNMTOOLS COMMAND] [OPTIONS] [ARGUMENTS]
-```
-In the above command, replace `/path/to/data` with the path to the directory you
-want to mount, and it will be mounted as the `/data` directory in the container.
-For example, if your genome data `genome.fa` is located in `./genome_data`, you
-can execute `abismalidx` by running:
-```console
-docker run -v ./genome_data:/data -w /data \
-  dnmtools abismalidx -v -t 4 genome.fa genome.idx
-```
-In the above command, `-w /data` specifies the working directory in the
-container, so the output `genome.idx` is saved in the `/data` directory,
-which corresponds to the `./genome_data` directory in the host
-machine. If you want to specify the output directory, use a command like below.
-```console
-docker run -v ./genome_data:/data -w /data \
-  -v ./genome_index:/output \
-  dnmtools abismalidx -v -t 4 genome.fa /output/genome.idx
-```
-When you need to access multiple directories, it might be useful to use the
-option `-v ./:/app -w /app`, which mounts the current directory
-to the `/app` directory in the container, which is alo set as the working
-directory. You can specify the paths in the same way you would from the
-working directory in the host machine. For example:
-```console
-docker run -v ./:/app -w /app \
-  dnmtools abismal -i genome_index/genome.idx -v -t 4 \
-  -o mapped_reads/output.sam \
-  reads/reads_1.fq reads/reads_1.fq
-```
-
-### Testing the install and use of docker image
-
-Run the following commands to test the installation and usage of the docker
-image of `dnmtools`.
-```console
-docker pull ghcr.io/smithlabcode/dnmtools:latest
-docker tag ghcr.io/smithlabcode/dnmtools:latest dnmtools:latest
-
-# Clone the repo to access test data
-git clone git@github.com:smithlabcode/dnmtools.git
-cd dnmtools
-
-# Run containers and save outputs in artifacts directory
-
-mkdir artifacts
-
-docker run -v ./:/app -w /app \
-  dnmtools abismalidx -v -t 1 data/tRex1.fa artifacts/tRex1.idx
-
-docker run -v ./:/app -w /app \
-  dnmtools simreads -seed 1 -o artifacts/simreads -n 10000 \
-  -m 0.01 -b 0.98 data/tRex1.fa
-
-docker run -v ./:/app -w /app \
-  dnmtools abismal -v -t 1 -i artifacts/tRex1.idx artifacts/simreads_{1,2}.fq
-```
-
-## Contacts and bug reports
+The documentation for DNMTools can be found
+[here](https://dnmtools.readthedocs.io).
+
+## Installation
+
+- **Linux**
+  The binary should work on almost any Linux system as recent as 2017: Ubuntu
+  16.04+, Debian 9+, Fedora 24+, openSUSE Leap 42.3+, and RHEL/CentOS 8+.
+  [Download](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0-Linux.tar.gz).
+
+- **Mac**
+  The Mac binary should work on any Mac hardware and macOS-13 (Ventura) or
+  newer.
+  [Download](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0-macOS.tar.gz).
+
+- **Conda**
+  ```console
+  conda install -c bioconda dnmtools
+  ```
+
+- **Build from source**
+  Get the source here:
+  [dnmtools-1.5.0.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0.tar.gz). Dependencies:
+  [GSL](http://www.gnu.org/software/gsl),
+  [HTSlib](https://github.com/samtools/htslib),
+  [libdeflate](https://github.com/ebiggers/libdeflate) and
+  [ZLib](https://github.com/madler/zlib). Installing GSL and HTSlib is usually enough.
+  See below for system-specific details.
+
+  Build DNMTools like this:
+  ```console
+  tar -xf dnmtools-1.5.0.tar.gz
+  cd dnmtools-1.5.0
+  ./configure --prefix=$HOME
+  make
+  make install
+  ```
+
+  Get dependencies and a compiler on (these might change):
+
+  Ubuntu/Debian
+  ```console
+  apt-get install build-essential htslib-dev libgsl-dev
+  ```
+
+  RedHat/Fedora
+  ```console
+  dnf install @c-development @development-tools htslib-devel gsl-devel awk
+  ```
+
+  Homebrew (see below)
+  ```console
+  brew install gcc htslib gsl
+  ```
+
+  Conda (see below)
+  ```console
+  conda create -n build-env -c conda-forge -c bioconda gcc gxx make autoconf automake htslib gsl && \
+  conda activate build-env
+  ```
+
+  If you used Homebrew or Conda, you might need to set additional environment
+  variables or run configure differently. For example with Homebrew:
+  ```console
+  ./configure CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib"
+  ```
+
+## Contact
 
 Andrew D. Smith
 andrewds@usc.edu
 
 ## Copyright and License Information
 
-Copyright (C) 2022-2024
+Copyright (C) 2022-2025
+
 Andrew D. Smith and Guilherme de Sena Brandine
 
 Authors of DNMTools: Andrew D. Smith and Guilherme de Sena Brandine
 
-Essential contributors: Ben Decato, Meng Zhou, Liz Ji, Terence Li,
-Jenny Qu, Qiang Song, Fang Fang and Masaru Nakajima
+Essential contributors: Ben Decato, Meng Zhou, Liz Ji, Terence Li, Jenny Qu,
+Qiang Song, Fang Fang and Masaru Nakajima
 
-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 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.
+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.