quickstart.md: updating ahead of v1.4.0 release.

Author: andrewdavidsmith

docs/content/quickstart.md

@@ -3,9 +3,19 @@ Installation
 
 ## Installation via conda
 
-Right now this is probably the easiest way. Dnmtools is among the
-bioconda recipes. If you know how to use conda and are setup to use
-bioconda, then you might simply be able to do:
+*Note (9/26/2023)* Although conda currently works, it seems that using
+`mamba` is more reliable. If you have `conda` installed, you can
+install mamba very easily by following instructions here:
+
+https://anaconda.org/conda-forge/mamba
+
+In the instructions below, replacing `conda` with `mamba` should work
+the same (and, in some cases, more reliably), but with mamba.
+
+Right now conda is probably the easiest way to install
+dnmtools. Dnmtools is among the bioconda recipes. If you know how to
+use conda and are setup to use bioconda, then you might simply be able
+to do:
 ```console
 $ conda install dnmtools
 ```
@@ -25,7 +35,6 @@ recommended by bioconda.
 * Bioconda: additional helpful setup instructions can be found
   [here](https://bioconda.github.io).
 
-
 If you encounter further problems, try creating a new environment for
 dnmtools within conda:
 ```console
@@ -42,32 +51,35 @@ would need to be activated when you want to use dnmtools.
 ### Required libraries
 
 * A recent compiler: most users will be building and installing this
-  software with GCC. We require a compiler that fully supports C++11,
-  so we recommend using at least GCC 5.8. 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.
+  software with GCC. We require a compiler that fully supports C++17,
+  so we recommend using at least GCC 8 (released in 2018). 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. On macOS and Ubuntu/Debian
+  systems, the brew and apt package managers can get you a recent
+  compiler easily. Any cluster or high-performance computing
+  environment should give you access to a recent compiler.
 * The GNU Scientific Library: this has always been required. 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, which can be installed through brew on macOS,
+  through apt on Linux (Ubuntu, Debian), or from source downloadable
+  [here](https://github.com/samtools/htslib).
 * The Zlib compression library: Most likely you already have this
   installed on your system. If not, it can be installed using apt on
   Linux (Ubuntu, Debian) through the package `zlib1g-dev`. On macOS,
   Zlib can be installed with brew.
-* The HTSlib library, which can be installed through brew on macOS,
-  through apt on Linux (Ubuntu, Debian), or from source downloadable
-  [here](https://github.com/samtools/htslib).
 
 ### Configuration
 
-* Download [dnmtools-1.3.0.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.3.0/dnmtools-1.3.0.tar.gz).
+* Download [dnmtools-1.4.0.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.4.0/dnmtools-1.4.0.tar.gz).
 * Unpack the archive:
 ```console
-$ tar -zxvf dnmtools-1.3.0.tar.gz
+$ tar -zxvf dnmtools-1.4.0.tar.gz
 ```
 * Move into the dnmtools directory and create a build directory:
 ```console
-$ cd dnmtools-1.3.0
+$ cd dnmtools-1.4.0
 $ mkdir build && cd build
 ```
 * Run the configuration script:
@@ -109,16 +121,23 @@ any arguments and you should see the list of available commands:
 ```console
 $ dnmtools
 ```
+If you want to do more extensive tests, you can run:
+```console
+$ make check
+```
+from the directory where you run `make`. This will to several tests of
+various commands within `dnmtools`, and might take some time.
 
 ## Using a clone of the repo
 
-Not recommended, but if you want to do it this way, we assume you know
-what you are doing. We strongly recommend using dnmtools through the
-latest stable release under the releases section on GitHub. Developers
-who wish to work on the latest commits, which are unstable, can
-compile the source using the `Makefile` available in the root of the
-source tree. If HTSLib and other libraries are available system-wide,
-compile by running:
+*This option is deprecated; we are no longer maintaining a Makefile
+that is not generated by `./configure`.* Not recommended, but if you
+want to do it this way, we assume you know what you are doing. We
+strongly recommend using dnmtools through the latest stable release
+under the releases section on GitHub. Developers who wish to work on
+the latest commits, which are unstable, can compile the source using
+the `Makefile` available in the root of the source tree. If HTSLib and
+other libraries are available system-wide, compile by running:
 ```console
 $ make
 ```