Documenting Docker offerings

MANUAL

@@ -99,6 +99,8 @@ Bowtie 2 is available from various package managers, notably Bioconda.
 With Bioconda installed, you should be able to install Bowtie 2 with
 conda install bowtie2.
 
+Binaries
+
 You can also download Bowtie 2 sources and binaries from the Download
 section of the Sourceforge site. Binaries are available for the x86_64
 architecture running Linux, Mac OS X, and Windows. FreeBSD users can
@@ -107,7 +109,18 @@ pkg install bowtie2. If you plan to compile Bowtie 2 yourself, make sure
 to get the source package, i.e., the filename that ends in
 "-source.zip".
 
-Building from source
+Docker
+
+Docker images with Bowtie 2 built in are created by BioContainers. These
+images can be found on Quay.io's biocontainers/bowtie2. For reference,
+Quay.io is an alternate registry to Docker Hub, andone can docker pull
+directly from it:
+
+    docker pull quay.io/biocontainers/bowtie2:2.5.3--py310ha0a81b8_0
+
+Alternately, for Apple Silicon or Intel/AMD users, there are
+community-made Dockerfiles created in late 2023 in the GitHub repository
+docker-bowtie2.
 
 Building from source
 

MANUAL.markdown

@@ -104,6 +104,9 @@ Bowtie 2 is available from various package managers, notably [Bioconda](https://
 With Bioconda installed, you should be able to install Bowtie 2 with `conda
 install bowtie2`.
 
+Binaries
+--------
+
 You can also download Bowtie 2 sources and binaries from the
 [Download] section of the Sourceforge site.  Binaries are available
 for the `x86_64` architecture running Linux, Mac OS X, and Windows.
@@ -112,9 +115,27 @@ using `pkg install bowtie2`. If you plan to compile Bowtie 2 yourself,
 make sure to get the source package, i.e., the filename that ends
 in "-source.zip".
 
+Docker
+------
+
+Docker images with Bowtie 2 built in
+are created by [BioContainers](https://github.com/BioContainers/containers).
+These images can be found on
+[Quay.io's `biocontainers/bowtie2`](https://quay.io/repository/biocontainers/bowtie2?tab=tags).
+For reference, [Quay.io](quay.io) is an alternate registry to Docker Hub,
+andone can `docker pull` directly from it:
+
+```bash
+docker pull quay.io/biocontainers/bowtie2:2.5.3--py310ha0a81b8_0
+```
+
+Alternately, for Apple Silicon or Intel/AMD users,
+there are community-made `Dockerfile`s
+created in late 2023 in the GitHub repository
+[docker-bowtie2](https://github.com/pmambrose/docker-bowtie2).
+
 Building from source
 --------------------
-Building from source
 
 Building Bowtie 2 from source requires a GNU-like environment with
 Clang/GCC, GNU Make and other basics. It should be possible to build

doc/manual.html

@@ -21,11 +21,72 @@
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 </head>
 <body>
 <h1>Table of Contents</h1>
@@ -45,6 +106,8 @@ <h1 class="title">Bowtie 2 Manual</h1>
 <li><a href="#obtaining-bowtie-2" id="toc-obtaining-bowtie-2">Obtaining
 Bowtie 2</a>
 <ul>
+<li><a href="#binaries" id="toc-binaries">Binaries</a></li>
+<li><a href="#docker" id="toc-docker">Docker</a></li>
 <li><a href="#building-from-source"
 id="toc-building-from-source">Building from source</a>
 <ul>
@@ -317,6 +380,7 @@ <h1 id="obtaining-bowtie-2">Obtaining Bowtie 2</h1>
 href="https://anaconda.org/bioconda/bowtie2">Bioconda</a>. With Bioconda
 installed, you should be able to install Bowtie 2 with
 <code>conda install bowtie2</code>.</p>
+<h2 id="binaries">Binaries</h2>
 <p>You can also download Bowtie 2 sources and binaries from the <a
 href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/">Download</a>
 section of the Sourceforge site. Binaries are available for the
@@ -325,8 +389,21 @@ <h1 id="obtaining-bowtie-2">Obtaining Bowtie 2</h1>
 <code>pkg install bowtie2</code>. If you plan to compile Bowtie 2
 yourself, make sure to get the source package, i.e., the filename that
 ends in "-source.zip".</p>
+<h2 id="docker">Docker</h2>
+<p>Docker images with Bowtie 2 built in are created by <a
+href="https://github.com/BioContainers/containers">BioContainers</a>.
+These images can be found on <a
+href="https://quay.io/repository/biocontainers/bowtie2?tab=tags">Quay.io's
+<code>biocontainers/bowtie2</code></a>. For reference, <a
+href="quay.io">Quay.io</a> is an alternate registry to Docker Hub,
+andone can <code>docker pull</code> directly from it:</p>
+<div class="sourceCode" id="cb1"><pre
+class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">docker</span> pull quay.io/biocontainers/bowtie2:2.5.3--py310ha0a81b8_0</span></code></pre></div>
+<p>Alternately, for Apple Silicon or Intel/AMD users, there are
+community-made <code>Dockerfile</code>s created in late 2023 in the
+GitHub repository <a
+href="https://github.com/pmambrose/docker-bowtie2">docker-bowtie2</a>.</p>
 <h2 id="building-from-source">Building from source</h2>
-<p>Building from source</p>
 <p>Building Bowtie 2 from source requires a GNU-like environment with
 Clang/GCC, GNU Make and other basics. It should be possible to build
 Bowtie 2 on most vanilla *NIX installations or on a Mac installation