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            <span id="subtitle">【记录】安装生信的代码编写环境</span>
          
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            <h1 id="seo-header">【记录】安装生信的代码编写环境</h1>
            
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                    Last updated on May 18, 2024 pm
                  
                
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                <h2 id="安装-vscode-web">安装 vscode-web</h2>
<ul>
<li>安装好 <a href="/DOCKER-an-zhuang-liu-cheng-ji-lu">docker</a></li>
<li><a href="/-ji-lu-SOCKS5-zhuan-QUIC">QUIC 转 SOCKS5</a></li>
</ul>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-built_in">mkdir</span> -p ~/app/vscode &amp;&amp; <span class="hljs-built_in">cd</span> ~/app/vscode &amp;&amp; nano docker-compose.yml<br>sudo docker-compose up -d &amp;&amp; sudo docker-compose logs<br></code></pre></td></tr></table></figure>
<figure class="highlight yml"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br></pre></td><td class="code"><pre><code class="hljs yml"><span class="hljs-attr">version:</span> <span class="hljs-string">&quot;2.1&quot;</span><br><span class="hljs-attr">services:</span><br>  <span class="hljs-attr">code-server:</span><br>    <span class="hljs-attr">image:</span> <span class="hljs-string">linuxserver/code-server:latest</span><br>    <span class="hljs-attr">container_name:</span> <span class="hljs-string">code-server</span><br>    <span class="hljs-attr">environment:</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">PUID=1000</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">PGID=1000</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">TZ=Asia/Shanghai</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">PASSWORD=password</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">SUDO_PASSWORD=password</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">PROXY_DOMAIN=code-server.my.domain</span> <span class="hljs-comment">#optional</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">DEFAULT_WORKSPACE=/config/workspace</span> <span class="hljs-comment">#optional</span><br>    <span class="hljs-attr">volumes:</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">./config:/config</span><br>    <span class="hljs-attr">ports:</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-number">2441</span><span class="hljs-string">:8443</span><br>    <span class="hljs-attr">restart:</span> <span class="hljs-string">unless-stopped</span><br></code></pre></td></tr></table></figure>
<h3 id="配置代理和中文">配置代理和中文</h3>
<ul>
<li>打开Visual Studio Code，点击Manage，在列表中选择Settings</li>
<li>在弹出的搜索框中输入&quot;proxy&quot;，即可看到代理的配置项&quot;Http:Proxy&quot;</li>
<li>宿主机获取docker0的ip: <code>ip address | grep docker0</code></li>
<li>然后docker内设置代理 <code>http://docker0的ip:port</code><br>
拓展内搜索zh-cn，安装中文界面拓展</li>
</ul>
<h3 id="安装-conda">安装 conda</h3>
<ul>
<li>回到WORKSPACE，ctrl+~ 调出终端</li>
<li><code>sudo sed -i 's/archive.ubuntu.com/mirrors.aliyun.com/g' /etc/apt/sources.list</code></li>
<li><code>sudo apt update</code></li>
<li><code>sudo apt install wget</code></li>
<li>安装 <a href="/-ji-lu--an-zhuang-conda-bing-geng-huan-qing-hua-yuan">conda</a></li>
</ul>
<h3 id="安装nodejs">安装nodejs</h3>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs bash">conda create -n node -c conda-forge nodejs<br>conda activate node<br>npm config <span class="hljs-built_in">set</span> registry https://registry.npmmirror.com<br></code></pre></td></tr></table></figure>
<h3 id="使用git">使用git</h3>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br></pre></td><td class="code"><pre><code class="hljs bash">npm create astro@latest<br>git config --global user.email <span class="hljs-string">&quot;youremail&quot;</span><br>git config --global user.name <span class="hljs-string">&quot;yourname&quot;</span><br>git branch -M main &amp;&amp; git add . &amp;&amp; git commit -m <span class="hljs-string">&#x27;Initial commit&#x27;</span><br>git remote add origin https://github.com/Limour-dev/chatGPT.git<br>git push --set-upstream origin main --force <span class="hljs-comment"># Creating a personal access token</span><br>git config --global credential.helper cache<br>git push<br></code></pre></td></tr></table></figure>
<h3 id="hello-world">hello world</h3>
<figure class="highlight js"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs js">---<br><span class="hljs-keyword">const</span> search = <span class="hljs-title class_">Astro</span>.<span class="hljs-property">url</span>.<span class="hljs-property">searchParams</span>.<span class="hljs-title function_">get</span>(<span class="hljs-string">&#x27;search&#x27;</span>)! || <span class="hljs-string">&#x27;&#x27;</span>;<br>---<br><span class="language-xml"><span class="hljs-tag">&lt;<span class="hljs-name">h1</span>&gt;</span>&#123;search&#125;<span class="hljs-tag">&lt;/<span class="hljs-name">h1</span>&gt;</span></span><br></code></pre></td></tr></table></figure>
<ul>
<li><a href="https://hexo.limour.top/go/#aHR0cHM6Ly9kb2NzLmFzdHJvLmJ1aWxkL2VuL2d1aWRlcy9zZXJ2ZXItc2lkZS1yZW5kZXJpbmcvI2VuYWJsaW5nLXNzci1pbi15b3VyLXByb2plY3Q=" rel="noopener external nofollow noreferrer">Enabling SSR in Your Project</a></li>
<li>编辑 chatGPT/src/pages/index.astro</li>
<li><code>npm run dev</code></li>
<li>访问 <code>https://vscode.domain/proxy/3000/?search=hello%20world</code> 进行测试</li>
</ul>
<h3 id="附加-win下集成conda">附加 win下集成conda</h3>
<ul>
<li>进入设置页面，搜索 <code>terminal.integrated.profiles.windows</code></li>
<li>编辑 <code>setting.json</code>, 给 <code>PowerShell</code> 中添加 <code>args</code></li>
<li><code>args</code> 的值可以通过查看 conda 快捷方式的属性来获取</li>
</ul>
<figure class="highlight json"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br></pre></td><td class="code"><pre><code class="hljs json"><span class="hljs-attr">&quot;PowerShell&quot;</span><span class="hljs-punctuation">:</span> <span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-attr">&quot;source&quot;</span><span class="hljs-punctuation">:</span> <span class="hljs-string">&quot;PowerShell&quot;</span><span class="hljs-punctuation">,</span><br>    <span class="hljs-attr">&quot;icon&quot;</span><span class="hljs-punctuation">:</span> <span class="hljs-string">&quot;terminal-powershell&quot;</span><span class="hljs-punctuation">,</span><br>    <span class="hljs-attr">&quot;args&quot;</span><span class="hljs-punctuation">:</span> <span class="hljs-punctuation">[</span><br>        <span class="hljs-string">&quot;$&#123;env:windir&#125;\\System32\\WindowsPowerShell\\v1.0\\powershell.exe&quot;</span><span class="hljs-punctuation">,</span><br>        <span class="hljs-string">&quot;-ExecutionPolicy ByPass -NoExit -Command&quot;</span><span class="hljs-punctuation">,</span><br>        <span class="hljs-string">&quot;\&quot;&amp; &#x27;$&#123;env:USERPROFILE&#125;\\miniconda3\\shell\\condabin\\conda-hook.ps1&#x27; ; conda activate &#x27;$&#123;env:USERPROFILE&#125;\\miniconda3&#x27; \&quot;&quot;</span><br>    <span class="hljs-punctuation">]</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
<h2 id="安装-Jupyter">安装 Jupyter</h2>
<h3 id="持久化镜像存储">持久化镜像存储</h3>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-built_in">mkdir</span> -p ~/datascience &amp;&amp; <span class="hljs-built_in">cd</span> ~/datascience<br>nano docker-compose.yml<br>sudo docker-compose up -d<br>sudo docker-compose logs<br>sudo docker <span class="hljs-built_in">cp</span> -a jupyterR:/opt /home/limour/upload/opt<br>sudo docker <span class="hljs-built_in">cp</span> -a jupyterR:/home/jovyan /home/limour/upload/home<br>sudo docker-compose down &amp;&amp; sudo docker volume prune<br></code></pre></td></tr></table></figure>
<figure class="highlight yml"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br></pre></td><td class="code"><pre><code class="hljs yml"><span class="hljs-attr">version:</span> <span class="hljs-string">&#x27;3.3&#x27;</span><br><span class="hljs-attr">services:</span><br>    <span class="hljs-attr">datascience-notebook:</span><br>        <span class="hljs-attr">ports:</span><br>            <span class="hljs-bullet">-</span> <span class="hljs-string">&#x27;57002:8888&#x27;</span><br>        <span class="hljs-attr">container_name:</span> <span class="hljs-string">jupyterR</span><br>        <span class="hljs-attr">restart:</span> <span class="hljs-string">always</span><br>        <span class="hljs-attr">image:</span> <span class="hljs-string">&#x27;jupyter/datascience-notebook:r-4.3.1&#x27;</span><br>        <span class="hljs-attr">command:</span> <span class="hljs-string">start-notebook.sh</span> <span class="hljs-string">--NotebookApp.token=&#x27;***&#x27;</span><br></code></pre></td></tr></table></figure>
<h3 id="启动镜像">启动镜像</h3>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs bash">nano docker-compose.yml<br>sudo <span class="hljs-built_in">chmod</span> 777 -R /home/limour/upload/<br>sudo docker-compose up -d<br>sudo docker-compose logs<br></code></pre></td></tr></table></figure>
<figure class="highlight yml"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br></pre></td><td class="code"><pre><code class="hljs yml"><span class="hljs-attr">version:</span> <span class="hljs-string">&#x27;3.3&#x27;</span><br><span class="hljs-attr">services:</span><br>    <span class="hljs-attr">datascience-notebook:</span><br>        <span class="hljs-attr">ports:</span><br>            <span class="hljs-bullet">-</span> <span class="hljs-string">&#x27;57002:8888&#x27;</span><br>        <span class="hljs-attr">container_name:</span> <span class="hljs-string">jupyterR</span><br>        <span class="hljs-attr">restart:</span> <span class="hljs-string">always</span><br>        <span class="hljs-attr">volumes:</span><br>            <span class="hljs-bullet">-</span> <span class="hljs-string">&#x27;/home/limour/upload:/home/jovyan/upload&#x27;</span><br>            <span class="hljs-bullet">-</span> <span class="hljs-string">&#x27;/home/limour/upload/opt:/opt&#x27;</span><br>            <span class="hljs-bullet">-</span> <span class="hljs-string">&#x27;/home/limour/upload/home:/home/jovyan&#x27;</span><br>        <span class="hljs-attr">image:</span> <span class="hljs-string">&#x27;jupyter/datascience-notebook:r-4.3.1&#x27;</span><br>        <span class="hljs-attr">command:</span> <span class="hljs-string">start-notebook.sh</span> <span class="hljs-string">--NotebookApp.token=&#x27;***&#x27;</span><br></code></pre></td></tr></table></figure>
<ul>
<li><a href="/-ji-lu--an-zhuang-npsfrp-fu-wu-duan-yu-ke-hu-duan">NPS内网穿透加NPM面板反代</a></li>
</ul>
<h3 id="R包镜像">R包镜像</h3>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs bash">nano .Rprofile<br>options()<span class="hljs-variable">$repos</span> <span class="hljs-comment">## 查看使用install.packages安装时的默认镜像</span><br>options()<span class="hljs-variable">$BioC_mirror</span> <span class="hljs-comment">##查看使用bioconductor的默认镜像</span><br></code></pre></td></tr></table></figure>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs R">options<span class="hljs-punctuation">(</span>BioC_mirror<span class="hljs-operator">=</span><span class="hljs-string">&quot;https://mirrors.ustc.edu.cn/bioc/&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-comment">##指定镜像，这个是中国科技大学镜像</span><br>options<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;repos&quot;</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>CRAN<span class="hljs-operator">=</span><span class="hljs-string">&quot;https://mirrors.tuna.tsinghua.edu.cn/CRAN/&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment">##指定install.packages安装镜像，这个是清华镜像</span><br>options<span class="hljs-punctuation">(</span>ggrepel.max.overlaps <span class="hljs-operator">=</span> <span class="hljs-literal">Inf</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
<h3 id="安装-R-内核">安装 R 内核</h3>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br></pre></td><td class="code"><pre><code class="hljs bash">conda create -n seurat -c conda-forge r-seurat=4.1.1 -y<br>conda activate seurat<br>conda install -c conda-forge r-tidyverse -y<br>conda install -c conda-forge r-irkernel -y<br>Rscript -e <span class="hljs-string">&quot;IRkernel::installspec(name=&#x27;seurat&#x27;, displayname=&#x27;r-seurat&#x27;)&quot;</span><br>conda install -c conda-forge r-devtools -y<br>Rscript -e <span class="hljs-string">&quot;BiocManager::install(&#x27;glmGamPoi&#x27;)&quot;</span><br>wget -e <span class="hljs-string">&quot;https_proxy=http://172.17.0.1:8580&quot;</span> https://github.com/chris-mcginnis-ucsf/DoubletFinder/archive/refs/heads/master.zip -O DoubletFinder-master.zip<br>Rscript -e <span class="hljs-string">&quot;devtools::install_local(&#x27;DoubletFinder-master.zip&#x27;)&quot;</span><br></code></pre></td></tr></table></figure>
<h3 id="安装-python-内核">安装 python 内核</h3>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs bash">conda create -n markdown2pptx -c conda-forge python -y<br>conda install -n markdown2pptx ipykernel -c conda-forge -y<br>conda run -n markdown2pptx python -m ipykernel install --user --name markdown2pptx<br>conda run -n markdown2pptx pip install -r requirements.txt -i https://pypi.tuna.tsinghua.edu.cn/simple<br></code></pre></td></tr></table></figure>
<h3 id="安装-Golang-内核">安装 Golang 内核</h3>
<ul>
<li>项目地址 <a href="https://hexo.limour.top/go/#aHR0cHM6Ly9naXRodWIuY29tL2dvcGhlcmRhdGEvZ29waGVybm90ZXM=" rel="noopener external nofollow noreferrer">gophernotes</a></li>
</ul>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br></pre></td><td class="code"><pre><code class="hljs bash">conda create -n golang -c conda-forge go -y<br>conda activate golang<br>go <span class="hljs-built_in">env</span> -w GO111MODULE=on<br>go <span class="hljs-built_in">env</span> -w GOPROXY=https://mirrors.aliyun.com/goproxy/<br>go install github.com/gopherdata/gophernotes@v0.7.5 <span class="hljs-comment">#去仓库查看最新版本号</span><br><span class="hljs-built_in">mkdir</span> -p ~/.local/share/jupyter/kernels/golang<br><span class="hljs-built_in">cd</span> ~/.local/share/jupyter/kernels/golang<br><span class="hljs-built_in">cp</span> <span class="hljs-string">&quot;<span class="hljs-subst">$(go env GOPATH)</span>&quot;</span>/pkg/mod/github.com/gopherdata/gophernotes@v0.7.5/kernel/* <span class="hljs-string">&quot;.&quot;</span><br><span class="hljs-built_in">chmod</span> +w ./kernel.json<br>sed <span class="hljs-string">&quot;s|gophernotes|<span class="hljs-subst">$(go env GOPATH)</span>/bin/gophernotes|&quot;</span> &lt; kernel.json.in &gt; kernel.json<br></code></pre></td></tr></table></figure>
<h3 id="安装-jupyter-ai-内核">安装 jupyter-ai 内核</h3>
<ul>
<li><a href="/Aggregating-Azure-and-OpenAI-APIs-with-OneAPI">获取端点和令牌</a></li>
<li>填写端点时尾部需要加上 <code>/v1</code></li>
</ul>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br></pre></td><td class="code"><pre><code class="hljs bash">conda create -n jupyter-ai -c conda-forge jupyter-ai-magics -y<br>conda install -n jupyter-ai -c conda-forge openai -y<br>conda install -n jupyter-ai ipykernel -c conda-forge -y<br>conda run -n jupyter-ai python -m ipykernel install --user --name jupyter-ai<br><span class="hljs-comment"># pip install --upgrade jupyterlab -i https://pypi.tuna.tsinghua.edu.cn/simple # 升级到 JupyterLab 4</span><br><span class="hljs-comment"># pip install jupyter_ai -i https://pypi.tuna.tsinghua.edu.cn/simple</span><br></code></pre></td></tr></table></figure>
<ul>
<li>启用拓展并配置端点和令牌</li>
</ul>
<figure class="highlight ipython"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs ipython">%load_ext jupyter_ai_magics<br>%env OPENAI_API_BASE=https://xxx/v1<br>%env OPENAI_API_KEY=sk-xxx<br></code></pre></td></tr></table></figure>
<ul>
<li>示例</li>
</ul>
<figure class="highlight ipython"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs ipython">%%ai chatgpt -f code<br>解决汉诺塔问题的函数<br></code></pre></td></tr></table></figure>
<p><img src="https://img.limour.top/2023/10/05/651e61bcdb7a1.webp" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt=""></p>
<h2 id="安装-rstudio">安装 rstudio</h2>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-built_in">mkdir</span> -p ~/app/rstudio &amp;&amp; <span class="hljs-built_in">cd</span> ~/app/rstudio &amp;&amp; nano docker-compose.yml<br>sudo docker-compose up -d &amp;&amp; sudo docker-compose logs<br></code></pre></td></tr></table></figure>
<figure class="highlight yml"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br></pre></td><td class="code"><pre><code class="hljs yml"><span class="hljs-attr">version:</span> <span class="hljs-string">&#x27;3&#x27;</span><br><span class="hljs-attr">services:</span><br>  <span class="hljs-attr">rstudio:</span><br>    <span class="hljs-attr">image:</span> <span class="hljs-string">dceoy/rstudio-server</span><br>    <span class="hljs-attr">container_name:</span> <span class="hljs-string">Rstudio</span><br>    <span class="hljs-attr">deploy:</span><br>      <span class="hljs-attr">resources:</span><br>        <span class="hljs-attr">limits:</span><br>          <span class="hljs-attr">cpus:</span> <span class="hljs-string">&#x27;0.50&#x27;</span><br>          <span class="hljs-attr">memory:</span> <span class="hljs-string">500M</span><br>        <span class="hljs-attr">reservations:</span><br>          <span class="hljs-attr">cpus:</span> <span class="hljs-string">&#x27;0.25&#x27;</span><br>          <span class="hljs-attr">memory:</span> <span class="hljs-string">200M</span><br>    <span class="hljs-attr">restart:</span> <span class="hljs-string">always</span><br>    <span class="hljs-attr">ports:</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-number">57022</span><span class="hljs-string">:8787</span><br>    <span class="hljs-attr">volumes:</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">/home/gene/zl_liu/rstudio:/home/rstudio</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">/home/gene/upload:/home/rstudio/upload</span><br>    <span class="hljs-attr">working_dir:</span> <span class="hljs-string">/home/rstudio</span><br></code></pre></td></tr></table></figure>
<h3 id="更改-R-版本">更改 R 版本</h3>
<ul>
<li>安装 <a href="/-ji-lu--an-zhuang-conda-bing-geng-huan-qing-hua-yuan">conda</a></li>
</ul>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-comment"># 容器内</span><br>conda create -n r_4_1_3 -c conda-forge r-base=4.1.3 -y<br>conda activate r_4_1_3<br>whereis R<br><span class="hljs-comment"># /home/rstudio/miniconda3/envs/r_4_1_3/bin/R</span><br><span class="hljs-comment"># 容器外</span><br>docker <span class="hljs-built_in">exec</span> -it Rstudio /bin/bash<br><span class="hljs-built_in">chmod</span> 777 -R  /etc/rstudio/<br><span class="hljs-built_in">exit</span> <br>nano -K /etc/rstudio/rserver.conf<br><span class="hljs-comment"># Server Configuration File</span><br>rsession-which-r=/home/rstudio/miniconda3/envs/r_4_1_3/bin/R<br>sudo docker-compose restart<br></code></pre></td></tr></table></figure>
<h3 id="安装-seurat">安装 seurat</h3>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-comment"># 进入terminal，以下操作均在terminal中进行</span><br><span class="hljs-built_in">export</span> R_LIBS_SITE=<span class="hljs-string">&quot;&quot;</span><br><span class="hljs-comment"># 在terminal中进入R</span><br>.libPaths(<span class="hljs-string">&#x27;/home/rstudio/miniconda3/envs/r_4_1_3/lib/R/library&#x27;</span>)<br>.libPaths() 确保没有其他路径<br>remove.packages(<span class="hljs-string">&quot;vctrs&quot;</span>)<br>install.packages(<span class="hljs-string">&quot;vctrs&quot;</span>)<br>install.packages(<span class="hljs-string">&#x27;Seurat&#x27;</span>)<br>remove.packages(<span class="hljs-string">&quot;cli&quot;</span>)<br>install.packages(<span class="hljs-string">&quot;cli&quot;</span>)<br>install.packages(<span class="hljs-string">&quot;tidyverse&quot;</span>)<br>install.packages(<span class="hljs-string">&quot;plotly&quot;</span>)<br>重启R session<br>library(tidyverse)<br>library(Seurat)<br></code></pre></td></tr></table></figure>
<h3 id="绘制-3D-umap">绘制 3D-umap</h3>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>plotly<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>Seurat<span class="hljs-punctuation">)</span><br>sample13 <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;~/upload/zl_liu/work/Prognosis/scRNA/sample13.rds&quot;</span><span class="hljs-punctuation">)</span><br>sample13 <span class="hljs-operator">&lt;-</span> RunUMAP<span class="hljs-punctuation">(</span>sample13<span class="hljs-punctuation">,</span> dims <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">10</span><span class="hljs-punctuation">,</span> n.components <span class="hljs-operator">=</span> <span class="hljs-number">3L</span><span class="hljs-punctuation">)</span><br>plot.data <span class="hljs-operator">&lt;-</span> FetchData<span class="hljs-punctuation">(</span>object <span class="hljs-operator">=</span> sample13<span class="hljs-punctuation">,</span> vars <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;UMAP_1&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;UMAP_2&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;UMAP_3&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;seurat_clusters&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>plot.data<span class="hljs-operator">$</span>label <span class="hljs-operator">&lt;-</span> paste<span class="hljs-punctuation">(</span>rownames<span class="hljs-punctuation">(</span>plot.data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># Plot your data, in this example my Seurat object had 21 clusters (0-20)</span><br>plot_ly<span class="hljs-punctuation">(</span>data <span class="hljs-operator">=</span> plot.data<span class="hljs-punctuation">,</span> <br>        x <span class="hljs-operator">=</span> <span class="hljs-operator">~</span>UMAP_1<span class="hljs-punctuation">,</span> y <span class="hljs-operator">=</span> <span class="hljs-operator">~</span>UMAP_2<span class="hljs-punctuation">,</span> z <span class="hljs-operator">=</span> <span class="hljs-operator">~</span>UMAP_3<span class="hljs-punctuation">,</span> <br>        color <span class="hljs-operator">=</span> <span class="hljs-operator">~</span>seurat_clusters<span class="hljs-punctuation">,</span> <br>        colors <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;lightseagreen&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;gray50&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;darkgreen&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;red4&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;red&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;turquoise4&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;black&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;yellow4&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;royalblue1&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;lightcyan3&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;peachpuff3&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;khaki3&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;gray20&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;orange2&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;royalblue4&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;yellow3&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;gray80&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;darkorchid1&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;lawngreen&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;plum2&quot;</span><span class="hljs-punctuation">,</span><br>                   <span class="hljs-string">&quot;darkmagenta&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">7</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><br>        type <span class="hljs-operator">=</span> <span class="hljs-string">&quot;scatter3d&quot;</span><span class="hljs-punctuation">,</span> <br>        mode <span class="hljs-operator">=</span> <span class="hljs-string">&quot;markers&quot;</span><span class="hljs-punctuation">,</span> <br>        marker <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>size <span class="hljs-operator">=</span> <span class="hljs-number">5</span><span class="hljs-punctuation">,</span> width<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-comment"># controls size of points</span><br>        text<span class="hljs-operator">=</span><span class="hljs-operator">~</span>label<span class="hljs-punctuation">,</span> <span class="hljs-comment">#This is that extra column we made earlier for which we will use for cell ID</span><br>        hoverinfo<span class="hljs-operator">=</span><span class="hljs-string">&quot;text&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-comment">#When you visualize your plotly object, hovering your mouse pointer over a point shows cell names</span><br></code></pre></td></tr></table></figure>
<h2 id="安装-notebook">安装 notebook</h2>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-built_in">mkdir</span> -p /home/limour/upload/home &amp;&amp; <span class="hljs-built_in">echo</span> `<span class="hljs-built_in">id</span> -u gene`:`<span class="hljs-built_in">id</span> -g gene`<br><span class="hljs-built_in">mkdir</span> -p ~/app/notebook &amp;&amp; <span class="hljs-built_in">cd</span> ~/app/notebook &amp;&amp; nano docker-compose.yml<br>sudo docker-compose up -d &amp;&amp; sudo docker-compose logs<br></code></pre></td></tr></table></figure>
<figure class="highlight yml"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br></pre></td><td class="code"><pre><code class="hljs yml"><span class="hljs-attr">version:</span> <span class="hljs-string">&#x27;3&#x27;</span><br><span class="hljs-attr">services:</span><br>  <span class="hljs-attr">notebook:</span><br>    <span class="hljs-attr">image:</span> <span class="hljs-string">jupyter/r-notebook</span><br>    <span class="hljs-attr">user:</span> <span class="hljs-string">&quot;1001:1001&quot;</span>  <span class="hljs-comment"># 替换为gene的UID和GID</span><br>    <span class="hljs-attr">container_name:</span> <span class="hljs-string">notebook</span><br>    <span class="hljs-attr">restart:</span> <span class="hljs-string">unless-stopped</span><br>    <span class="hljs-attr">extra_hosts:</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">&#x27;host.docker.internal:host-gateway&#x27;</span><br>    <span class="hljs-attr">environment:</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">DOCKER_STACKS_JUPYTER_CMD=nbclassic</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">TZ=Asia/Shanghai</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">JUPYTER_GATEWAY_REQUEST_TIMEOUT=600</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">JUPYTER_GATEWAY_CONNECT_TIMEOUT=600</span><br>    <span class="hljs-attr">ports:</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">&#x27;57002:8888&#x27;</span><br>    <span class="hljs-attr">volumes:</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">&#x27;/home/limour/upload:/home/jovyan/upload&#x27;</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">&#x27;/home/limour/upload/home:/home/jovyan&#x27;</span><br>      <span class="hljs-bullet">-</span> <span class="hljs-string">&#x27;/dev/shm:/home/jovyan/tmp&#x27;</span><br>    <span class="hljs-attr">command:</span> <span class="hljs-string">start-notebook.py</span> <span class="hljs-string">--NotebookApp.token=&#x27;***&#x27;</span><br></code></pre></td></tr></table></figure>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br></pre></td><td class="code"><pre><code class="hljs bash">conda init<br><span class="hljs-built_in">source</span> activate<br>conda config --add envs_dirs /home/jovyan/upload/envs<br>conda create -n mamba conda-forge::mamba=1.5.7<br><span class="hljs-built_in">source</span> activate mamba<br></code></pre></td></tr></table></figure>
<figure class="highlight nginx"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs nginx"><span class="hljs-attribute">proxy_connect_timeout</span>   <span class="hljs-number">600s</span>;<br><span class="hljs-attribute">proxy_read_timeout</span>      <span class="hljs-number">600s</span>;<br><span class="hljs-attribute">proxy_send_timeout</span>      <span class="hljs-number">600s</span>;<br><span class="hljs-attribute">proxy_buffering</span>         <span class="hljs-literal">off</span>;<br></code></pre></td></tr></table></figure>
<h3 id="R">R</h3>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-built_in">source</span> activate mamba<br>mamba create -n THCA_24_03_14 conda-forge::r-base=4.3.3<br>mamba install -n THCA_24_03_14 conda-forge::r-irkernel=1.3.2<br>mamba run -n THCA_24_03_14 Rscript -e <span class="hljs-string">&quot;IRkernel::installspec(name=&#x27;THCA_24_03_14&#x27;, displayname=&#x27;THCA_24_03_14&#x27;)&quot;</span><br><span class="hljs-built_in">source</span> activate THCA_24_03_14<br></code></pre></td></tr></table></figure>
<h3 id="proxychains">proxychains</h3>
<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br></pre></td><td class="code"><pre><code class="hljs bash"><span class="hljs-built_in">source</span> activate mamba<br>mamba install conda-forge::unzip<br>mkidr -p ~/dev &amp;&amp; mkidr -p ~/etc &amp;&amp; <span class="hljs-built_in">cd</span> ~/dev<br>wget https://github.com/rofl0r/proxychains-ng/archive/refs/heads/master.zip<br>unzip master.zip<br><span class="hljs-built_in">mv</span> proxychains-ng-master proxychains-ng &amp;&amp; <span class="hljs-built_in">cd</span> proxychains-ng &amp;&amp; make<br><span class="hljs-built_in">cat</span> &lt;&lt; <span class="hljs-string">EOF &gt;$HOME/etc/proxychains4.conf</span><br><span class="hljs-string">[ProxyList]</span><br><span class="hljs-string">socks5  `cat /etc/hosts | grep host.docker.internal | awk &#x27;&#123;print $1&#125;&#x27;` 8580</span><br><span class="hljs-string">EOF</span><br><span class="hljs-built_in">alias</span> proxychains=<span class="hljs-string">&#x27;$HOME/dev/proxychains-ng/proxychains4 -q -f $HOME/etc/proxychains4.conf&#x27;</span><br>proxychains curl https://b.limour.top<br></code></pre></td></tr></table></figure>
<h2 id="附加-windows端口映射">附加 windows端口映射</h2>
<figure class="highlight powershell"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs powershell">netsh interface portproxy add v4tov4 listenaddress=<span class="hljs-number">0.0</span>.<span class="hljs-number">0.0</span> listenport=<span class="hljs-number">57002</span> connectaddress=<span class="hljs-number">192.168</span>.<span class="hljs-number">243.129</span> connectport=<span class="hljs-number">57002</span><br>netsh interface portproxy show v4tov4<br></code></pre></td></tr></table></figure>
<ul>
<li>防火墙入站规则放行端口<code>57002</code></li>
<li>假设宿主物理机是 <code>192.168.10.247</code>, 其内部的虚拟机是 <code>192.168.243.129</code></li>
<li>局域网内其他物理机即可访问 <code>http://192.168.10.247:57002/nbclassic/tree?token=xxx</code></li>
</ul>

                
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      scrollSmooth    : true,
      includeTitleTags: true,
      headingsOffset  : -boardTop,
    }, CONFIG.toc));
    if (toc.find('.toc-list-item').length > 0) {
      toc.css('visibility', 'visible');
    }

    Fluid.events.registerRefreshCallback(function() {
      if ('tocbot' in window) {
        tocbot.refresh();
        var toc = jQuery('#toc');
        if (toc.length === 0 || !tocbot) {
          return;
        }
        if (toc.find('.toc-list-item').length > 0) {
          toc.css('visibility', 'visible');
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      }
    });
  });
</script>


  <script src=https://lib.baomitu.com/clipboard.js/2.0.11/clipboard.min.js></script>

  <script>Fluid.plugins.codeWidget();</script>


<script>
  Fluid.utils.createScript('https://jscdn.limour.top/npm/anchor-js@4.3.1/anchor.min.js', function() {
    window.anchors.options = {
      placement: CONFIG.anchorjs.placement,
      visible  : CONFIG.anchorjs.visible
    };
    if (CONFIG.anchorjs.icon) {
      window.anchors.options.icon = CONFIG.anchorjs.icon;
    }
    var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
    var res = [];
    for (var item of el) {
      res.push('.markdown-body > ' + item.trim());
    }
    if (CONFIG.anchorjs.placement === 'left') {
      window.anchors.options.class = 'anchorjs-link-left';
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    window.anchors.add(res.join(', '));

    Fluid.events.registerRefreshCallback(function() {
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        anchors.removeAll();
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        for (var item of el) {
          res.push('.markdown-body > ' + item.trim());
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        if (CONFIG.anchorjs.placement === 'left') {
          anchors.options.class = 'anchorjs-link-left';
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        anchors.add(res.join(', '));
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  });
</script>


  <script>Fluid.plugins.imageCaption();</script>

  <script  src="/js/local-search.js" ></script>


<!-- 主题的启动项，将它保持在最底部 -->
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<script  src="/js/boot.js" ></script>


  <noscript>
    <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  </noscript>
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</html>