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README.md: updating obtain/install/build instructions
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README.md

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@@ -23,28 +23,25 @@ The documentation for DNMTools can be found
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## Installation
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- **Linux**
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The binary should work on almost any Linux system as recent as 2017: Ubuntu
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16.04+, Debian 9+, Fedora 24+, openSUSE Leap 42.3+, and RHEL/CentOS 8+.
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[Download](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0-Linux.tar.gz).
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[binary](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0-Linux.tar.gz).
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Should work on any Linux distribution since roughly 2017.
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- **Mac**
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The Mac binary should work on any Mac hardware and macOS-13 (Ventura) or
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newer.
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[Download](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0-macOS.tar.gz).
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[binary](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0-macOS.tar.gz).
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Should work on any Mac hardware and macOS-13 (Ventura) or newer.
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- **Conda**
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```console
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conda install -c bioconda dnmtools
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```
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- **Build from source**
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Get the source here:
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- **Source**
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[dnmtools-1.5.0.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0.tar.gz). Dependencies:
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[GSL](http://www.gnu.org/software/gsl),
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[HTSlib](https://github.com/samtools/htslib),
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[libdeflate](https://github.com/ebiggers/libdeflate) and
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[ZLib](https://github.com/madler/zlib). Installing GSL and HTSlib is usually enough.
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See below for system-specific details.
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[ZLib](https://github.com/madler/zlib). Installing HTSlib as a package
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should also give you ZLib and libdeflate. System-specific details below.
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Build DNMTools like this:
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```console
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make install
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```
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Get dependencies and a compiler on (these might change):
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To get dependencies and a compiler on (these might with OS/package updates):
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Ubuntu/Debian
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```console
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dnf install @c-development @development-tools htslib-devel gsl-devel awk
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```
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Homebrew (see below)
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Homebrew (see notes below)
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```console
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brew install gcc htslib gsl
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```
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Conda (see below)
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Conda (see notes below)
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```console
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conda create -n build-env -c conda-forge -c bioconda gcc gxx make autoconf automake htslib gsl && \
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conda create -n build-env -c conda-forge -c bioconda \
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gcc gxx make autoconf automake htslib gsl zlib binutils && \
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conda activate build-env
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```
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If you used Homebrew or Conda, you might need to set additional environment
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variables or run configure differently. For example with Homebrew:
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Notes: If you use only Homebrew or only Conda to setup your environment, you
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could need additional dependencies, and some of what I listed you might
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already have. You might need to set additional environment variables or run
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configure differently. For example with Homebrew:
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```console
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./configure CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib"
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```

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