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            <h1 id="seo-header">Docker：部署数据科学栈Jupyter</h1>
            
            
              <div class="markdown-body">
                
                <h2 id="持久化镜像存储"><a href="#持久化镜像存储" class="headerlink" title="持久化镜像存储"></a>持久化镜像存储</h2><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-4.1.3&#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>mkdir -p ~&#x2F;datascience &amp;&amp; cd ~&#x2F;datascience</li>
<li>nano docker-compose.yml</li>
<li>sudo docker-compose up -d</li>
<li>sudo docker-compose logs</li>
<li>sudo docker cp -a jupyterR:&#x2F;opt &#x2F;home&#x2F;limour&#x2F;upload&#x2F;opt</li>
<li>sudo docker cp -a jupyterR:&#x2F;home&#x2F;jovyan &#x2F;home&#x2F;limour&#x2F;upload&#x2F;home</li>
<li>sudo docker-compose down &amp;&amp; sudo docker volume prune</li>
</ul>
<h2 id="启动镜像"><a href="#启动镜像" class="headerlink" title="启动镜像"></a>启动镜像</h2><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></pre></td><td class="code"><pre><code class="hljs R">version<span class="hljs-operator">:</span> <span class="hljs-string">&#x27;3.3&#x27;</span><br>services<span class="hljs-operator">:</span><br>    datascience<span class="hljs-operator">-</span>notebook<span class="hljs-operator">:</span><br>        ports<span class="hljs-operator">:</span><br>            <span class="hljs-operator">-</span> <span class="hljs-string">&#x27;57002:8888&#x27;</span><br>        container_name<span class="hljs-operator">:</span> jupyterR<br>        restart<span class="hljs-operator">:</span> always<br>        volumes<span class="hljs-operator">:</span><br>            <span class="hljs-operator">-</span> <span class="hljs-string">&#x27;/home/limour/upload:/home/jovyan/upload&#x27;</span><br>            <span class="hljs-operator">-</span> <span class="hljs-string">&#x27;/home/limour/upload/opt/opt:/opt&#x27;</span><br>            <span class="hljs-operator">-</span> <span class="hljs-string">&#x27;/home/limour/upload/home/jovyan:/home/jovyan&#x27;</span><br>        image<span class="hljs-operator">:</span> <span class="hljs-string">&#x27;jupyter/datascience-notebook:r-4.1.3&#x27;</span><br>        command<span class="hljs-operator">:</span> start<span class="hljs-operator">-</span>notebook.sh <span class="hljs-operator">-</span><span class="hljs-operator">-</span>NotebookApp.token<span class="hljs-operator">=</span><span class="hljs-string">&#x27;***&#x27;</span><br></code></pre></td></tr></table></figure>

<ul>
<li>nano docker-compose.yml</li>
<li>sudo chmod 777 -R &#x2F;home&#x2F;limour&#x2F;upload&#x2F;</li>
<li>sudo docker-compose up -d</li>
<li>sudo docker-compose logs</li>
<li>NPS内网穿透加NPM面板反代</li>
</ul>
<h2 id="R包镜像"><a href="#R包镜像" class="headerlink" title="R包镜像"></a>R包镜像</h2><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>

<ul>
<li>nano .Rprofile</li>
<li>options()$repos ## 查看使用install.packages安装时的默认镜像</li>
<li>options()$BioC_mirror ##查看使用bioconductor的默认镜像</li>
</ul>
<h2 id="conda镜像"><a href="#conda镜像" class="headerlink" title="conda镜像"></a>conda镜像</h2><p><a target="_blank" rel="noopener" href="https://mirror.tuna.tsinghua.edu.cn/help/anaconda/">Anaconda 镜像使用帮助</a>；<a target="_blank" rel="noopener" href="https://occdn.limour.top/2285.html">Docker安装A面板</a></p>
<ul>
<li>nano .condarc</li>
<li>conda clean -i</li>
<li>conda create -n seurat -c conda-forge r-seurat&#x3D;4.1.1 -y</li>
<li>conda activate seurat</li>
<li>conda install -c conda-forge r-tidyverse -y</li>
<li>conda install -c conda-forge r-irkernel -y</li>
<li>Rscript -e “IRkernel::installspec(name&#x3D;’seurat’, displayname&#x3D;’r-seurat’)”</li>
<li>wget -e “https_proxy&#x3D;<a target="_blank" rel="noopener" href="http://172.17.0.1:20171/">http://172.17.0.1:20171</a>“ <a target="_blank" rel="noopener" href="https://github.com/chris-mcginnis-ucsf/DoubletFinder/archive/refs/heads/master.zip">https://github.com/chris-mcginnis-ucsf/DoubletFinder/archive/refs/heads/master.zip</a> -O DoubletFinder-master.zip</li>
<li>上面的”https_proxy&#x3D;<a target="_blank" rel="noopener" href="http://172.17.0.1:20171"来自容器A面板">http://172.17.0.1:20171&quot;来自容器A面板</a></li>
</ul>

                
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