Browse Source

rebuild docs

master
james hadfield 2 years ago
parent
commit
b0ca00e48e
  1. 6
      docs/introduction/install.html
  2. 6
      docs/introduction/install/index.html
  3. 27
      docs/releases/changelog.html
  4. 27
      docs/releases/changelog/index.html

6
docs/introduction/install.html

@ -59,6 +59,10 @@
For best results, please use Node.js version 10.</p>
<p>We highly recommend using <a href="https://conda.io/docs/">Conda</a> to manage environments, i.e. use Conda to create an environment with Node.js installed where you can use Auspice.
It's possible to use other methods, but this documentation presupposes that you have Conda installed.</p>
<p>To run package scripts, the <a href="https://en.wikipedia.org/wiki/Bash_(Unix_shell)"><code>bash</code> shell</a> and the <a href="https://en.wikipedia.org/wiki/Env"><code>env</code></a> command need to be in your <code>PATH</code>.
You should already have them on Unix-like systems including Linux and macOS.
If you are working from Windows, you can run the installation under Git Bash, MSYS2, or Cygwin.
You can also use the Windows Subsystem Linux for a fuller Linux environment.</p>
<h2><a class="anchor" aria-hidden="true" id="create-a-conda-environment"></a><a href="#create-a-conda-environment" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Create a Conda Environment</h2>
<pre><code class="hljs css language-bash">conda create --name auspice nodejs=10
<span class="hljs-built_in">source</span> activate auspice
@ -100,4 +104,4 @@ auspice --<span class="hljs-built_in">help</span>
</code></pre>
<p>Updating Auspice should only require pulling the new version from GitHub -- it shouldn't require any <code>npm</code> commands.
You will, however, have to re-build Auspice whenever the client-related code has changed, via <code>auspice build</code>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/overview"><span class="arrow-prev"></span><span>Overview</span></a><a class="docs-next button" href="/auspice/introduction/how-to-run"><span>How to Run Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#create-a-conda-environment">Create a Conda Environment</a></li><li><a href="#install-auspice-from-npm">Install Auspice from npm</a></li><li><a href="#installing-from-source">Installing from Source</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 2/12/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/overview"><span class="arrow-prev"></span><span>Overview</span></a><a class="docs-next button" href="/auspice/introduction/how-to-run"><span>How to Run Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#create-a-conda-environment">Create a Conda Environment</a></li><li><a href="#install-auspice-from-npm">Install Auspice from npm</a></li><li><a href="#installing-from-source">Installing from Source</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

6
docs/introduction/install/index.html

@ -59,6 +59,10 @@
For best results, please use Node.js version 10.</p>
<p>We highly recommend using <a href="https://conda.io/docs/">Conda</a> to manage environments, i.e. use Conda to create an environment with Node.js installed where you can use Auspice.
It's possible to use other methods, but this documentation presupposes that you have Conda installed.</p>
<p>To run package scripts, the <a href="https://en.wikipedia.org/wiki/Bash_(Unix_shell)"><code>bash</code> shell</a> and the <a href="https://en.wikipedia.org/wiki/Env"><code>env</code></a> command need to be in your <code>PATH</code>.
You should already have them on Unix-like systems including Linux and macOS.
If you are working from Windows, you can run the installation under Git Bash, MSYS2, or Cygwin.
You can also use the Windows Subsystem Linux for a fuller Linux environment.</p>
<h2><a class="anchor" aria-hidden="true" id="create-a-conda-environment"></a><a href="#create-a-conda-environment" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Create a Conda Environment</h2>
<pre><code class="hljs css language-bash">conda create --name auspice nodejs=10
<span class="hljs-built_in">source</span> activate auspice
@ -100,4 +104,4 @@ auspice --<span class="hljs-built_in">help</span>
</code></pre>
<p>Updating Auspice should only require pulling the new version from GitHub -- it shouldn't require any <code>npm</code> commands.
You will, however, have to re-build Auspice whenever the client-related code has changed, via <code>auspice build</code>.</p>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 10/17/2019</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/overview"><span class="arrow-prev"></span><span>Overview</span></a><a class="docs-next button" href="/auspice/introduction/how-to-run"><span>How to Run Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#create-a-conda-environment">Create a Conda Environment</a></li><li><a href="#install-auspice-from-npm">Install Auspice from npm</a></li><li><a href="#installing-from-source">Installing from Source</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>
</span></div></article></div><div class="docLastUpdate"><em>Last updated on 2/12/2020</em></div><div class="docs-prevnext"><a class="docs-prev button" href="/auspice/introduction/overview"><span class="arrow-prev"></span><span>Overview</span></a><a class="docs-next button" href="/auspice/introduction/how-to-run"><span>How to Run Auspice</span><span class="arrow-next"></span></a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#prerequisites">Prerequisites</a></li><li><a href="#create-a-conda-environment">Create a Conda Environment</a></li><li><a href="#install-auspice-from-npm">Install Auspice from npm</a></li><li><a href="#installing-from-source">Installing from Source</a></li></ul></nav></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><a href="/auspice/"><img style="padding-left:20px" src="/auspice/img/logo-light.svg" alt="Auspice" width="66" height="58"/></a></div><div><h5>External Links</h5><a href="https://github.com/nextstrain/auspice">GitHub repo</a><a href="https://www.npmjs.com/package/auspice">NPM package</a><a href="https://nextstrain.org">Nextstrain</a></div><div><h5>Contact Us</h5><a href="mailto:hello@nextstrain.org">email</a><a href="https://twitter.com/hamesjadfield">twitter</a></div></section><section class="copyright">Website built by <a href="https://twitter.com/hamesjadfield">James Hadfield</a> using <a href="https://docusaurus.io">Docusaurus</a></section><section class="copyright">If you use auspice, please cite <a href="https://doi.org/10.1093/bioinformatics/bty407">Hadfield et al., 2018</a></section><section class="copyright">Copyright © 2014-2020 Richard Neher &amp; Trevor Bedford</section></footer></div></body></html>

27
docs/releases/changelog.html
File diff suppressed because it is too large
View File

27
docs/releases/changelog/index.html
File diff suppressed because it is too large
View File

Loading…
Cancel
Save