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sellth committed Sep 18, 2024
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2 changes: 1 addition & 1 deletion admin/getting-access/index.html
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Expand Up @@ -3395,7 +3395,7 @@ <h3 id="form">Form<a class="headerlink" href="#form" title="Permanent link">&par
<span class="md-icon" title="Last update">
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Expand Up @@ -4059,7 +4059,7 @@ <h2 id="previous-maintenance">Previous Maintenance<a class="headerlink" href="#p
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Expand Up @@ -3441,7 +3441,7 @@ <h3 id="credentials-policies">Credentials Policies<a class="headerlink" href="#c
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2 changes: 1 addition & 1 deletion best-practice/bashrc-guide/index.html
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Expand Up @@ -3147,7 +3147,7 @@ <h1 id="bashrc-guide"><code>~/.bashrc</code> Guide<a class="headerlink" href="#b
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2 changes: 1 addition & 1 deletion best-practice/env-modules/index.html
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Expand Up @@ -3374,7 +3374,7 @@ <h2 id="auto-loading-a-set-of-modules">Auto-loading a set of Modules<a class="he
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2 changes: 1 addition & 1 deletion best-practice/project-structure/index.html
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Expand Up @@ -3535,7 +3535,7 @@ <h2 id="example-wrapper-scripts-in-home-option-22">Example: Wrapper Scripts in H
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2 changes: 1 addition & 1 deletion best-practice/screen-tmux/index.html
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Expand Up @@ -3353,7 +3353,7 @@ <h2 id="fix-a-broken-screen-session">Fix a broken screen session<a class="header
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2 changes: 1 addition & 1 deletion best-practice/software-craftmanship/index.html
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Expand Up @@ -3350,7 +3350,7 @@ <h2 id="understand-bash-and-shell-exit-codes">Understand Bash and Shell Exit Cod
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22 changes: 12 additions & 10 deletions best-practice/software-installation-with-conda/index.html
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Expand Up @@ -3236,25 +3236,27 @@ <h2 id="conda">Conda<a class="headerlink" href="#conda" title="Permanent link">&
to do so. We will provide you with a description on how to install conda and how
to use it. Of course there are many online resources that you can also use.
Please find a list at the end of the document.</p>
<p>Also note that some system-level software is managed through environment modules.</p>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>Following a change in their terms of service Anaconda Inc. has started to demand payment from research institutions
for using both Anaconda, Miniconda, and the defaults channel. As a consequence,
usage of this software is prohibited and we're recommending the alternative free "miniforge" distribution instead.</p>
</div>
<h2 id="premise">Premise<a class="headerlink" href="#premise" title="Permanent link">&para;</a></h2>
<p>When you logged into the cluster, please make sure that you also executed <code>srun</code> to log into a computation node and perform the software installation there.</p>
<h2 id="installing-conda">Installing conda<a class="headerlink" href="#installing-conda" title="Permanent link">&para;</a></h2>
<div class="highlight"><pre><span></span><code>hpc-login-1:~$<span class="w"> </span>srun<span class="w"> </span>--mem<span class="o">=</span>5G<span class="w"> </span>--pty<span class="w"> </span>bash<span class="w"> </span>-i
hpc-cpu-123:~$<span class="w"> </span>wget<span class="w"> </span>https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
hpc-cpu-123:~$<span class="w"> </span>bash<span class="w"> </span>Miniconda3-latest-Linux-x86_64.sh<span class="w"> </span>-b<span class="w"> </span>-f<span class="w"> </span>-p<span class="w"> </span><span class="nv">$HOME</span>/work/miniconda
hpc-cpu-123:~$<span class="w"> </span><span class="nb">eval</span><span class="w"> </span><span class="s2">&quot;</span><span class="k">$(</span>/<span class="nv">$HOME</span>/work/miniconda/bin/conda<span class="w"> </span>shell.bash<span class="w"> </span>hook<span class="k">)</span><span class="s2">&quot;</span>
hpc-cpu-123:~$<span class="w"> </span>wget<span class="w"> </span>https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
hpc-cpu-123:~$<span class="w"> </span>bash<span class="w"> </span>Miniforge3-Linux-x86_64.sh<span class="w"> </span>-b<span class="w"> </span>-f<span class="w"> </span>-p<span class="w"> </span><span class="nv">$HOME</span>/work/miniforge
hpc-cpu-123:~$<span class="w"> </span><span class="nb">eval</span><span class="w"> </span><span class="s2">&quot;</span><span class="k">$(</span>/<span class="nv">$HOME</span>/work/miniforge/bin/conda<span class="w"> </span>shell.bash<span class="w"> </span>hook<span class="k">)</span><span class="s2">&quot;</span>
hpc-cpu-123:~$<span class="w"> </span>conda<span class="w"> </span>init
hpc-cpu-123:~$<span class="w"> </span>conda<span class="w"> </span>config<span class="w"> </span>--set<span class="w"> </span>auto_activate_base<span class="w"> </span><span class="nb">false</span>
</code></pre></div>
<p>This will install conda to <code>$HOME/work/miniconda</code>.
<p>This will install conda to <code>$HOME/work/miniforge</code>.
You can change the path to your liking, but please note that your <code>$HOME</code> folder has limited space.
The <code>work</code> subfolder however has a bigger quota. More about this <a href="../../storage/home-quota/">here</a>.</p>
<p>To make bioinformatics software available, we have to add the <code>bioconda</code> and
some other channels to the conda configuration:</p>
<p>To make bioinformatics software available, we have to add the <code>bioconda</code> channel to the conda configuration:</p>
<div class="highlight"><pre><span></span><code>hpc-cpu-123:~$<span class="w"> </span>conda<span class="w"> </span>config<span class="w"> </span>--add<span class="w"> </span>channels<span class="w"> </span>bioconda
hpc-cpu-123:~$<span class="w"> </span>conda<span class="w"> </span>config<span class="w"> </span>--add<span class="w"> </span>channels<span class="w"> </span>default
hpc-cpu-123:~$<span class="w"> </span>conda<span class="w"> </span>config<span class="w"> </span>--add<span class="w"> </span>channels<span class="w"> </span>conda-forge
</code></pre></div>
<h2 id="installing-software-with-conda">Installing software with conda<a class="headerlink" href="#installing-software-with-conda" title="Permanent link">&para;</a></h2>
<p>Installing packages with conda is straight forward:</p>
Expand Down Expand Up @@ -3327,7 +3329,7 @@ <h2 id="creating-an-environment">Creating an environment<a class="headerlink" hr
<span class="md-icon" title="Last update">
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2 changes: 1 addition & 1 deletion best-practice/temp-files/index.html
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Expand Up @@ -3315,7 +3315,7 @@ <h3 id="use-bash-traps">Use Bash Traps<a class="headerlink" href="#use-bash-trap
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2 changes: 1 addition & 1 deletion connecting/advanced-ssh/linux/index.html
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Expand Up @@ -3440,7 +3440,7 @@ <h2 id="x11">X11<a class="headerlink" href="#x11" title="Permanent link">&para;<
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2 changes: 1 addition & 1 deletion connecting/advanced-ssh/overview/index.html
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Expand Up @@ -3127,7 +3127,7 @@ <h1 id="advanced-ssh-usage">Advanced SSH usage<a class="headerlink" href="#advan
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2 changes: 1 addition & 1 deletion connecting/connecting-windows/index.html
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Expand Up @@ -3276,7 +3276,7 @@ <h2 id="connecting-from-within-mdccharite-network">Connecting from within MDC/Ch
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
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<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">August 29, 2024</span>
<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">September 18, 2024</span>
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2 changes: 1 addition & 1 deletion connecting/connecting/index.html
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Expand Up @@ -3308,7 +3308,7 @@ <h2 id="i-have-problems-connecting">I have problems connecting<a class="headerli
<span class="md-icon" title="Last update">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
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<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">August 29, 2024</span>
<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">September 18, 2024</span>
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2 changes: 1 addition & 1 deletion connecting/connection-problems/index.html
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Expand Up @@ -3308,7 +3308,7 @@ <h2 id="i-can-connect-but-i-get-a-password-prompt">I can connect, but I get a pa
<span class="md-icon" title="Last update">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
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<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">August 29, 2024</span>
<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">September 18, 2024</span>
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2 changes: 1 addition & 1 deletion connecting/from-external/index.html
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Expand Up @@ -3376,7 +3376,7 @@ <h3 id="charite-vdi-not-recommended">Charité VDI (Not recommended)<a class="hea
<span class="md-icon" title="Last update">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
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<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">August 29, 2024</span>
<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">September 18, 2024</span>
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2 changes: 1 addition & 1 deletion connecting/generate-key/linux/index.html
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Expand Up @@ -3226,7 +3226,7 @@ <h2 id="submit-your-key">Submit Your Key<a class="headerlink" href="#submit-your
<span class="md-icon" title="Last update">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
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<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">August 29, 2024</span>
<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">September 18, 2024</span>
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2 changes: 1 addition & 1 deletion connecting/generate-key/windows/index.html
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Expand Up @@ -3271,7 +3271,7 @@ <h2 id="submit-your-key">Submit Your Key<a class="headerlink" href="#submit-your
<span class="md-icon" title="Last update">
<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
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<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">August 29, 2024</span>
<span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-date">September 18, 2024</span>
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