@@ -23,28 +23,25 @@ The documentation for DNMTools can be found
2323## Installation
2424
2525- ** Linux**
26- The binary should work on almost any Linux system as recent as 2017: Ubuntu
27- 16.04+, Debian 9+, Fedora 24+, openSUSE Leap 42.3+, and RHEL/CentOS 8+.
28- [ Download] ( https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0-Linux.tar.gz ) .
26+ [ binary] ( https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0-Linux.tar.gz ) .
27+ Should work on any Linux distribution since roughly 2017.
2928
3029- ** Mac**
31- The Mac binary should work on any Mac hardware and macOS-13 (Ventura) or
32- newer.
33- [ Download] ( https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0-macOS.tar.gz ) .
30+ [ binary] ( https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0-macOS.tar.gz ) .
31+ Should work on any Mac hardware and macOS-13 (Ventura) or newer.
3432
3533- ** Conda**
3634 ``` console
3735 conda install -c bioconda dnmtools
3836 ```
3937
40- - ** Build from source**
41- Get the source here:
38+ - ** Source**
4239 [ dnmtools-1.5.0.tar.gz] ( https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0.tar.gz ) . Dependencies:
4340 [ GSL] ( http://www.gnu.org/software/gsl ) ,
4441 [ HTSlib] ( https://github.com/samtools/htslib ) ,
4542 [ libdeflate] ( https://github.com/ebiggers/libdeflate ) and
46- [ ZLib] ( https://github.com/madler/zlib ) . Installing GSL and HTSlib is usually enough.
47- See below for system -specific details.
43+ [ ZLib] ( https://github.com/madler/zlib ) . Installing HTSlib as a package
44+ should also give you ZLib and libdeflate. System -specific details below .
4845
4946 Build DNMTools like this:
5047 ``` console
@@ -55,7 +52,7 @@ The documentation for DNMTools can be found
5552 make install
5653 ```
5754
58- Get dependencies and a compiler on (these might change ):
55+ To get dependencies and a compiler on (these might with OS/package updates ):
5956
6057 Ubuntu/Debian
6158 ``` console
@@ -67,19 +64,22 @@ The documentation for DNMTools can be found
6764 dnf install @c-development @development-tools htslib-devel gsl-devel awk
6865 ```
6966
70- Homebrew (see below)
67+ Homebrew (see notes below)
7168 ``` console
7269 brew install gcc htslib gsl
7370 ```
7471
75- Conda (see below)
72+ Conda (see notes below)
7673 ``` console
77- conda create -n build-env -c conda-forge -c bioconda gcc gxx make autoconf automake htslib gsl && \
74+ conda create -n build-env -c conda-forge -c bioconda \
75+ gcc gxx make autoconf automake htslib gsl zlib binutils && \
7876 conda activate build-env
7977 ```
8078
81- If you used Homebrew or Conda, you might need to set additional environment
82- variables or run configure differently. For example with Homebrew:
79+ Notes: If you use only Homebrew or only Conda to setup your environment, you
80+ could need additional dependencies, and some of what I listed you might
81+ already have. You might need to set additional environment variables or run
82+ configure differently. For example with Homebrew:
8383 ``` console
8484 ./configure CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib"
8585 ```
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