update download options

Author: shenwei356

download/index.html

@@ -326,22 +326,15 @@
 </li>
 
           <li class="md-nav__item">
-  <a href="#method-2-install-via-conda-latest-stable-version" class="md-nav__link">
-    Method 2: Install via conda (latest stable version)
+  <a href="#method-2-install-via-conda-or-pixi-latest-stable-version" class="md-nav__link">
+    Method 2: Install via conda or pixi (latest stable version)
   </a>
 
 </li>
 
           <li class="md-nav__item">
-  <a href="#method-3-install-via-homebrew-might-not-be-latest-stable-version" class="md-nav__link">
-    Method 3: Install via homebrew (might not be latest stable version)
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#method-4-for-go-developer-latest-stabledev-version" class="md-nav__link">
-    Method 4: For Go developer (latest stable/dev version)
+  <a href="#method-3-install-via-homebrew-latest-stable-version" class="md-nav__link">
+    Method 3: Install via homebrew (latest stable version)
   </a>
 
 </li>
@@ -563,22 +556,15 @@
 </li>
 
           <li class="md-nav__item">
-  <a href="#method-2-install-via-conda-latest-stable-version" class="md-nav__link">
-    Method 2: Install via conda (latest stable version)
+  <a href="#method-2-install-via-conda-or-pixi-latest-stable-version" class="md-nav__link">
+    Method 2: Install via conda or pixi (latest stable version)
   </a>
 
 </li>
 
           <li class="md-nav__item">
-  <a href="#method-3-install-via-homebrew-might-not-be-latest-stable-version" class="md-nav__link">
-    Method 3: Install via homebrew (might not be latest stable version)
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#method-4-for-go-developer-latest-stabledev-version" class="md-nav__link">
-    Method 4: For Go developer (latest stable/dev version)
+  <a href="#method-3-install-via-homebrew-latest-stable-version" class="md-nav__link">
+    Method 3: Install via homebrew (latest stable version)
   </a>
 
 </li>
@@ -755,15 +741,16 @@ <h4 id="method-1-download-binaries-latest-stable-version">Method 1: Download bin
 <p><strong>For windows</strong>, just copy <code>seqkit.exe</code> to <code>C:\WINDOWS\system32</code>.</p>
 </li>
 </ol>
-<h4 id="method-2-install-via-conda-latest-stable-version">Method 2: Install via conda (latest stable version)  <a href="https://anaconda.org/bioconda/seqkit"><img alt="Anaconda Cloud" src="https://anaconda.org/bioconda/seqkit/badges/version.svg" /></a> <a href="https://anaconda.org/bioconda/seqkit"><img alt="downloads" src="https://anaconda.org/bioconda/seqkit/badges/downloads.svg" /></a></h4>
-<pre><code>conda install -c bioconda seqkit
+<h4 id="method-2-install-via-conda-or-pixi-latest-stable-version">Method 2: Install via conda or pixi (latest stable version)  <a href="https://anaconda.org/bioconda/seqkit"><img alt="Anaconda Cloud" src="https://anaconda.org/bioconda/seqkit/badges/version.svg" /></a> <a href="https://anaconda.org/bioconda/seqkit"><img alt="downloads" src="https://anaconda.org/bioconda/seqkit/badges/downloads.svg" /></a></h4>
+<pre><code># conda or mamba
+conda install -c bioconda seqkit
+
+# pixi
+pixi global install -c bioconda seqkit
 </code></pre>
-<h4 id="method-3-install-via-homebrew-might-not-be-latest-stable-version">Method 3: Install via <a href="https://brew.sh/">homebrew</a> (might not be latest stable version)</h4>
+<h4 id="method-3-install-via-homebrew-latest-stable-version">Method 3: Install via <a href="https://brew.sh/">homebrew</a> (latest stable version)</h4>
 <pre><code>brew install seqkit
 </code></pre>
-<h4 id="method-4-for-go-developer-latest-stabledev-version">Method 4: For Go developer (latest stable/dev version)</h4>
-<pre><code>go get -u github.com/shenwei356/seqkit/v2/seqkit/
-</code></pre>
 <h4 id="method-5-docker-based-installation-might-not-be-latest-stable-versio">Method 5: Docker based installation (might not be latest stable versio)</h4>
 <p><a href="https://docs.docker.com/engine/installation/#supported-platforms">Install Docker</a></p>
 <p>git clone this repo:</p>
@@ -787,22 +774,15 @@ <h4 id="method-6-compiling-from-source-latest-stabledev-version">Method 6: Compi
 #   source ~/.bashrc
 export PATH=$PATH:$HOME/go/bin
 
-
-# ------------- the latest stable version -------------
-
-go get -v -u github.com/shenwei356/seqkit/seqkit
-
-# The executable binary file is located in:
-#   ~/go/bin/seqkit
-# You can also move it to anywhere in the $PATH
-mkdir -p $HOME/bin
-cp ~/go/bin/seqkit $HOME/bin/
-
-# --------------- the development version --------------
+# --------------- the stable/development version --------------
 
 git clone https://github.com/shenwei356/seqkit
 cd seqkit/seqkit/
-go build
+
+# optionally choose a release
+# git check v2.10.0
+
+go build -trimpath -ldflags="-s -w" -tags netgo
 
 # The executable binary file is located in:
 #   ./seqkit

index.html

@@ -281,6 +281,40 @@
     Installation
   </a>
 
+    <nav class="md-nav" aria-label="Installation">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#method-1-download-binaries" class="md-nav__link">
+    Method 1: Download binaries
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#method-2-install-via-pixi" class="md-nav__link">
+    Method 2: Install via Pixi
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#method-3-install-via-conda" class="md-nav__link">
+    Method 3: Install via conda
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#method-4-install-via-homebrew" class="md-nav__link">
+    Method 4: Install via homebrew
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
 
         <li class="md-nav__item">
@@ -511,6 +545,40 @@
     Installation
   </a>
 
+    <nav class="md-nav" aria-label="Installation">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#method-1-download-binaries" class="md-nav__link">
+    Method 1: Download binaries
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#method-2-install-via-pixi" class="md-nav__link">
+    Method 2: Install via Pixi
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#method-3-install-via-conda" class="md-nav__link">
+    Method 3: Install via conda
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#method-4-install-via-homebrew" class="md-nav__link">
+    Method 4: Install via homebrew
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
 
         <li class="md-nav__item">
@@ -623,10 +691,17 @@ <h2 id="features">Features</h2>
 </li>
 </ul>
 <h2 id="installation">Installation</h2>
-<p>Go to <a href="http://bioinf.shenwei.me/seqkit/download">Download Page</a> for more download options and changelogs, or
-install via conda:</p>
+<h4 id="method-1-download-binaries">Method 1: Download binaries</h4>
+<p>Go to <a href="http://bioinf.shenwei.me/seqkit/download">Download Page</a>, where you can find download links to various platforms.</p>
+<h4 id="method-2-install-via-pixi">Method 2: Install via Pixi</h4>
+<pre><code>pixi global install -c bioconda seqkit
+</code></pre>
+<h4 id="method-3-install-via-conda">Method 3: Install via conda</h4>
 <pre><code>conda install -c bioconda seqkit
 </code></pre>
+<h4 id="method-4-install-via-homebrew">Method 4: Install via homebrew</h4>
+<pre><code>brew install seqkit
+</code></pre>
 <h2 id="subcommands">Subcommands</h2>
 <table>
 <thead>

search/search_index.json

@@ -2445,15 +2445,16 @@ <h2 id="fx2tab-tab2fx">fx2tab &amp; tab2fx</h2>
      or FASTQ, except when flag -n/--name is on. This is for format compatibility.
 
 Usage:
-  seqkit fx2tab [flags]
+  seqkit fx2tab [flags] 
 
 Flags:
   -a, --alphabet               print alphabet letters
   -q, --avg-qual               print average quality of a read
-  -B, --base-content strings   print base content. (case ignored, multiple values supported) e.g. -B AT -B N
+  -B, --base-content strings   print base content. (case ignored, multiple values supported) e.g. -B AT
+                               -B N. Note that the denominator is the sequence length
   -C, --base-count strings     print base count. (case ignored, multiple values supported) e.g. -C AT -C N
   -I, --case-sensitive         calculate case sensitive base content/sequence hash
-  -g, --gc                     print GC content
+  -g, --gc                     print GC content, i.e., (G+C)/(G+C+A+T)
   -G, --gc-skew                print GC-Skew
   -H, --header-line            print header line
   -h, --help                   help for fx2tab