diff --git a/MANUAL b/MANUAL index 58fb9f0b..9f226f0d 100644 --- a/MANUAL +++ b/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 diff --git a/MANUAL.markdown b/MANUAL.markdown index 9a81b4e2..809be366 100644 --- a/MANUAL.markdown +++ b/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 diff --git a/doc/manual.html b/doc/manual.html index f729020c..7c153dbb 100644 --- a/doc/manual.html +++ b/doc/manual.html @@ -21,11 +21,72 @@ vertical-align: middle; } .display.math{display: block; text-align: center; margin: 0.5rem auto;} + /* CSS for syntax highlighting */ + pre > code.sourceCode { white-space: pre; position: relative; } + pre > code.sourceCode > span { line-height: 1.25; } + pre > code.sourceCode > span:empty { height: 1.2em; } + .sourceCode { overflow: visible; } + code.sourceCode > span { color: inherit; text-decoration: inherit; } + div.sourceCode { margin: 1em 0; } + pre.sourceCode { margin: 0; } + @media screen { + div.sourceCode { overflow: auto; } + } + @media print { + pre > code.sourceCode { white-space: pre-wrap; } + pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; } + } + pre.numberSource code + { counter-reset: source-line 0; } + pre.numberSource code > span + { position: relative; left: -4em; counter-increment: source-line; } + pre.numberSource code > span > a:first-child::before + { content: counter(source-line); + position: relative; left: -1em; text-align: right; vertical-align: baseline; + border: none; display: inline-block; + -webkit-touch-callout: none; -webkit-user-select: none; + -khtml-user-select: none; -moz-user-select: none; + -ms-user-select: none; user-select: none; + padding: 0 4px; width: 4em; + color: #aaaaaa; + } + pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; } + div.sourceCode + { } + @media screen { + pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; } + } + code span.al { color: #ff0000; font-weight: bold; } /* Alert */ + code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */ + code span.at { color: #7d9029; } /* Attribute */ + code span.bn { color: #40a070; } /* BaseN */ + code span.bu { color: #008000; } /* BuiltIn */ + code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */ + code span.ch { color: #4070a0; } /* Char */ + code span.cn { color: #880000; } /* Constant */ + code span.co { color: #60a0b0; font-style: italic; } /* Comment */ + code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */ + code span.do { color: #ba2121; font-style: italic; } /* Documentation */ + code span.dt { color: #902000; } /* DataType */ + code span.dv { color: #40a070; } /* DecVal */ + code span.er { color: #ff0000; font-weight: bold; } /* Error */ + code span.ex { } /* Extension */ + code span.fl { color: #40a070; } /* Float */ + code span.fu { color: #06287e; } /* Function */ + code span.im { color: #008000; font-weight: bold; } /* Import */ + code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */ + code span.kw { color: #007020; font-weight: bold; } /* Keyword */ + code span.op { color: #666666; } /* Operator */ + code span.ot { color: #007020; } /* Other */ + code span.pp { color: #bc7a00; } /* Preprocessor */ + code span.sc { color: #4070a0; } /* SpecialChar */ + code span.ss { color: #bb6688; } /* SpecialString */ + code span.st { color: #4070a0; } /* String */ + code span.va { color: #19177c; } /* Variable */ + code span.vs { color: #4070a0; } /* VerbatimString */ + code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */ -

Table of Contents

@@ -45,6 +106,8 @@

Bowtie 2 Manual

  • Obtaining Bowtie 2