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<!DOCTYPE html>
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<head>
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<title>Usage — Bioconda documentation</title>
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<img alt="_images/bioconda.png" src="_images/bioconda.png" />
<p><strong>Bioconda</strong> lets you install thousands of software packages related to
biomedical research using the <a class="reference external" href="https://conda.io">conda</a> package manager.</p>
<p><strong>NOTE</strong>: <em>Bioconda supports only Linux (64-bit and AArch64) and macOS (x86_64 and ARM64)</em></p>
<section id="usage">
<h1>Usage<a class="headerlink" href="#usage" title="Link to this heading">¶</a></h1>
<p>First, <a class="reference external" href="https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html">install conda</a>.</p>
<p>Then perform a one-time set up of Bioconda with the following commands. This
will modify your <code class="file docutils literal notranslate"><span class="pre">~/.condarc</span></code> file:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">config</span> <span class="o">--</span><span class="n">add</span> <span class="n">channels</span> <span class="n">bioconda</span>
<span class="n">conda</span> <span class="n">config</span> <span class="o">--</span><span class="n">add</span> <span class="n">channels</span> <span class="n">conda</span><span class="o">-</span><span class="n">forge</span>
<span class="n">conda</span> <span class="n">config</span> <span class="o">--</span><span class="nb">set</span> <span class="n">channel_priority</span> <span class="n">strict</span>
</pre></div>
</div>
<p>If you have used Bioconda in the past, note that the recommended configuration
has changed over the years. You should run the above commands to ensure your
settings follow the current recommendations.</p>
<details><summary>How have the recommendations changed?</summary><div id=recommendation-changes class="details"><p><i>How have the recommendations changed?</i><a class="headerlink" title="Permalink" href="#recommendation-changes">¶</a></p><p>In June 2022, the additional command <code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">config</span> <span class="pre">--set</span>
<span class="pre">channel_priority_strict</span></code> was added; see the <a class="reference external" href="#explain-commands">explanation of commands below</a> for details.</p>
</div></details><details><summary>What did these commands do?</summary><div id=explain-commands class="details"><p><i>What did these commands do?</i><a class="headerlink" title="Permalink" href="#explain-commands">¶</a></p><p>In general, running <code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">config</span></code> modifies your condarc file which can be
found at <code class="docutils literal notranslate"><span class="pre">~/.condarc</span></code> by default.</p>
<p>The first three commands add channels, from lowest to highest priority.
<strong>The order is important</strong> to avoid problems with solving dependencies:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">config</span> <span class="o">--</span><span class="n">add</span> <span class="n">channels</span> <span class="n">defaults</span>
<span class="n">conda</span> <span class="n">config</span> <span class="o">--</span><span class="n">add</span> <span class="n">channels</span> <span class="n">bioconda</span>
<span class="n">conda</span> <span class="n">config</span> <span class="o">--</span><span class="n">add</span> <span class="n">channels</span> <span class="n">conda</span><span class="o">-</span><span class="n">forge</span>
</pre></div>
</div>
<ul class="simple">
<li><p>The <code class="docutils literal notranslate"><span class="pre">defaults</span></code> channel is the one set by default in a new installation of
conda. It should be set to the lowest priority.</p></li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">bioconda</span></code> channel enables installation of packages related to
biomedical research.</p></li>
<li><p>The <code class="docutils literal notranslate"><span class="pre">conda-forge</span></code> channel (see <a class="reference external" href="https://conda-forge.org/docs/index.html">docs</a>) enables installation of
general-purpose packages. Since <code class="docutils literal notranslate"><span class="pre">bioconda</span></code> heavily depends on the
<code class="docutils literal notranslate"><span class="pre">conda-forge</span></code> channel, it is set to highest priority.</p></li>
</ul>
<p>This command:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">config</span> <span class="o">--</span><span class="nb">set</span> <span class="n">channel_priority</span> <span class="n">strict</span>
</pre></div>
</div>
<p>avoids cryptic errors when tryng to install. It ensures that the channel
priority configured above is respected when solving dependencies. See <a class="reference external" href="https://conda-forge.org/docs/user/tipsandtricks.html">this
section of the conda-forge docs</a> for more info.</p>
</div></details><details><summary>What if I don't want to modify my condarc?</summary><div id=do-not-modify-condarc class="details"><p><i>What if I don't want to modify my condarc?</i><a class="headerlink" title="Permalink" href="#do-not-modify-condarc">¶</a></p><blockquote>
<div><p>Sometimes you want to specify the channel priority directly in the
<code class="docutils literal notranslate"><span class="pre">conda</span></code> command-line call, and do not want to change the condarc file
with the suggested <code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">config</span></code> commands above.</p>
<p>To match the above recommendations, you need to append the following
arguments to any <code class="docutils literal notranslate"><span class="pre">conda</span></code> calls:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">--</span><span class="n">channel</span> <span class="n">conda</span><span class="o">-</span><span class="n">forge</span> <span class="o">--</span><span class="n">channel</span> <span class="n">bioconda</span> <span class="o">--</span><span class="n">strict</span><span class="o">-</span><span class="n">channel</span><span class="o">-</span><span class="n">priority</span>
</pre></div>
</div>
<p>For example, to create an environment containing bwa and
samtools without running the <code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">config</span></code> commands above, then you
would use:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">create</span> <span class="o">-</span><span class="n">n</span> <span class="n">myenv</span> <span class="n">samtools</span> <span class="n">bwa</span> \
<span class="o">--</span><span class="n">channel</span> <span class="n">conda</span><span class="o">-</span><span class="n">forge</span> \
<span class="o">--</span><span class="n">channel</span> <span class="n">bioconda</span> \
<span class="o">--</span><span class="n">channel</span> <span class="n">defaults</span> \
<span class="o">--</span><span class="n">strict</span><span class="o">-</span><span class="n">channel</span><span class="o">-</span><span class="n">priority</span>
</pre></div>
</div>
<p>Note that conda interprets channels on the command line in order
of <em>decreasing</em> priority (in contrast to <code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">config</span></code>, where they are
listed in increasing priority).</p>
<p>See the <a class="reference external" href="#explain-commands">explanation of commands</a> for details on what
these arguments do.</p>
</div></blockquote>
</div></details><p>Now you can use <code class="docutils literal notranslate"><span class="pre">conda</span></code> to install and use any of the <a class="reference external" href="conda-package_index.html">packages available in
bioconda</a>.</p>
<details><summary>How do I speed up package installation?</summary><div class="details"><p><i>How do I speed up package installation?</i></p><p>Sometimes conda can spend a lot of time trying to solve dependencies for an
environment. See <a class="reference internal" href="faqs.html#speedup"><span class="std std-ref">How do I speed up package installation?</span></a> in the FAQs for some options to improve this.</p>
</div></details><details><summary>How do I get Docker containers of packages?</summary><div id=how-do-i-get-containers class="details"><p><i>How do I get Docker containers of packages?</i><a class="headerlink" title="Permalink" href="#how-do-i-get-containers">¶</a></p><blockquote>
<div><p>Every conda package in Bioconda has a corresponding Docker <a class="reference external" href="https://biocontainers.pro">BioContainer</a>
automatically created and uploaded to <a class="reference external" href="https://quay.io/organization/biocontainers">Quay.io</a>. A list of these and other
containers can be found at the <a class="reference external" href="https://biocontainers.pro/#/registry">BioContainers Registry</a>. For example:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">docker</span> <span class="n">pull</span> <span class="n">quay</span><span class="o">.</span><span class="n">io</span><span class="o">/</span><span class="n">biocontainers</span><span class="o">/</span><span class="n">samtools</span><span class="p">:</span><span class="mf">1.15.1</span><span class="o">--</span><span class="n">h1170115_0</span>
</pre></div>
</div>
<p>If you have docker installed, you do not need any additional configuration.</p>
</div></blockquote>
</div></details></section>
<section id="overview">
<h1>Overview<a class="headerlink" href="#overview" title="Link to this heading">¶</a></h1>
<p>While Bioconda channel is the primary output for users, it takes a team of
contributors and additional infrastructure to make it all happen. The entire
system consists of the components illustrated in the diagram below.</p>
<a class="reference internal image-reference" href="_images/bioconda-dag.png"><img alt="_images/bioconda-dag.png" src="_images/bioconda-dag.png" style="width: 80%;" />
</a>
<p><strong>Legend</strong> (starting from the bottom):</p>
<p><span class="circlednumber">①</span> Over 1800 contributors who add,
modify, update, and maintain recipes and packages</p>
<details><summary>Details</summary><div class="details"><p><i>Details</i></p><p><a class="reference external" href="https://github.com/bioconda/bioconda-recipes/graphs/contributors">Contributors</a> to
Bioconda add new recipes or update existing recipes by opening pull
requests to GitHub. Contributors might include:</p>
<ul class="simple">
<li><p>authors of the software</p></li>
<li><p>Bioconda core team</p></li>
<li><p>anyone interested creating a conda package</p></li>
</ul>
<p>There’s even a Bioconda bot that watches common places
for updates (like CRAN, PyPI, GitHub releases) and submits a pull
request with the update for other contributors to review.</p>
</div></details><p><span class="circlednumber">②</span> A repository of recipes hosted on GitHub</p>
<details><summary>Details</summary><div class="details"><p><i>Details</i></p><p>The full history of all recipes is stored in the <a class="reference external" href="https://github.com/bioconda/bioconda-recipes">repository of recipes</a>
on GitHub.</p>
<p>Contributors and Bioconda core team coordinate, collaborate, and
help each other out via comments on GitHub in issues and pull requests
which are tested (see <span class="circlednumber">③</span>). The goal is to get a working
package that satisfies the Bioconda policies.</p>
</div></details><p><span class="circlednumber">③</span> A build system that turns each recipes into a conda
package and a Docker container</p>
<details><summary>Details</summary><div class="details"><p><i>Details</i></p><p>Every time changes are pushed to a GitHub pull request (e.g., new
recipe or updates to recipe), all of these changes are automatically built
and tested. The results are reported back to the GitHub pull request page.
Contributors work together to fix any issues (which are tested again) and
the process repeats until all tests pass.</p>
<p>Our <a class="reference external" href="https://github.com/bioconda/bioconda-utils">build system</a>, <a class="conda-package reference internal" href="recipes/bioconda-utils/README.html#package-bioconda-utils" title="bioconda-utils package"><code class="xref any conda conda-package docutils literal notranslate"><span class="pre">bioconda-utils</span></code></a>, orchestrates the various building
and testing steps on CI infrastructure like CircleCI, Azure Pipelines, and
GitHub Actions. The output consists of both a <a class="reference external" href="https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/packages.html">conda package</a> and
a <a class="reference external" href="https://biocontainers.pro">Biocontainer</a> that can be inspected before merging the pull request.</p>
</div></details><p><span class="circlednumber">④</span> A repository of packages and a registry of containers
containing over 8000 bioinformatics packages</p>
<details><summary>Details</summary><div class="details"><p><i>Details</i></p><p>When all tests pass and the pull request is merged into the main branch,
two things happen:</p>
<ol class="arabic simple">
<li><p>A final conda package is built and uploaded to the <a class="reference external" href="https://anaconda.org/bioconda">Bioconda channel on
anaconda.org</a> on anaconda.org.</p></li>
<li><p>That same conda package is installed into a Docker container which is
then uploaded to the <a class="reference external" href="https://quay.io/biocontainers">Biocontainers registry</a>.</p></li>
</ol>
</div></details><p><span class="circlednumber">⑤</span> Users can then use the package with <code class="xref any docutils literal notranslate"><span class="pre">conda</span> <span class="pre">install</span></code> or <code class="xref any docutils literal notranslate"><span class="pre">docker</span> <span class="pre">pull</span></code></p>
<details><summary>Details</summary><div class="details"><p><i>Details</i></p><p>See above for how to configure the conda channels. Using docker containers
just needs docker installed.</p>
</div></details><section id="package-downloads">
<h2>Package downloads<a class="headerlink" href="#package-downloads" title="Link to this heading">¶</a></h2>
<p>The following plots show the recent usage of Bioconda in terms of number of
downloads.</p>
<p>You can <a class="reference external" href="conda-package_index.html">browse all packages</a> in the Bioconda
channel.</p>
<div style="width: 100%" id="download_plot"></div>
<div style="width: 100%" id="package_plot"></div>
<script>
window.onload = async function () {
function buildDownloadsPlot(bioconda_data) {
let spec = {
"$schema": "https://vega.github.io/schema/vega-lite/v5.json",
"description": "Total bioconda downloads.",
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"mark": "line",
"encoding": {
"y": {
"field": "total",
"type": "quantitative",
"title": "total downloads",
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"domainMin": { "expr": "min-1000" },
"domainMax": { "expr": "max+1000" }
}
},
"x": { "field": "date", "timeUnit": "yearmonthdate", "title": "date", "axis": { "labelAngle": -15 } },
"color": { "value": "#43AF4E" },
"tooltip": { "field": "total" }
}
};
vegaEmbed('#download_plot', spec);
}
// Download download plot data
try {
const bioconda_resp = await fetch("https://raw.githubusercontent.com/bioconda/bioconda-stats/data/package-downloads/anaconda.org/bioconda/channel.tsv")
if (!bioconda_resp.ok) {
throw new Error(`Fetching failed with HTTP code ${bioconda_resp.status}.`);
}
const bioconda_data = await bioconda_resp.text();
buildDownloadsPlot(bioconda_data);
} catch (err) {
console.error("An error occurred while building channel downloads plot: ", err)
}
function buildTopPackagesPlot(package_data) {
let package_spec = {
"$schema": "https://vega.github.io/schema/vega-lite/v5.json",
"description": "Top downloaded packages.",
"title": "Top 20 packages",
"data": {
"values": package_data,
"format": { "type": "tsv", "parse": { "total": "number" } }
},
"transform": [
{
"window": [{ "op": "rank", "as": "rank" }],
"sort": [{ "field": "total", "order": "descending" }]
},
{
"filter": "datum.rank <= 20"
}
],
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"mark": "bar",
"encoding": {
"x": { "field": "total", "type": "quantitative", "title": "total downloads" },
"y": { "field": "package", "sort": "-x", "type": "nominal", "title": "package" },
"color": { "value": "#43AF4E" },
"tooltip": { "field": "total" }
}
};
vegaEmbed('#package_plot', package_spec);
};
// Download package plot data
try {
const package_resp = await fetch("https://raw.githubusercontent.com/bioconda/bioconda-stats/data/package-downloads/anaconda.org/bioconda/packages.tsv")
if (!package_resp.ok) {
throw new Error(`Fetching failed with HTTP code ${package_resp.status}.`);
}
const package_data = await package_resp.text();
buildTopPackagesPlot(package_data);
} catch (err) {
console.error("An error occurred while building top packages plot: ", err)
}
}
</script></section>
</section>
<section id="acknowledgments">
<h1>Acknowledgments<a class="headerlink" href="#acknowledgments" title="Link to this heading">¶</a></h1>
<p>The Bioconda channel could not exist without support from:</p>
<ul class="simple">
<li><p><a class="reference external" href="https://www.anaconda.com/">Anaconda, Inc</a> in the form of providing
unlimited (in time and space) storage for packages in the channel.</p></li>
<li><p><a class="reference external" href="https://circleci.com/">Circle CI</a> via an open source plan including free
Linux and MacOS builds.</p></li>
<li><p>Amazon Web Services in the form of storage for BioContainers as well as
compute credits.</p></li>
<li><p><a class="reference external" href="https://azure.microsoft.com/en-us/services/devops/pipelines/">Azure DevOps</a> open source plan</p></li>
<li><p><a class="reference external" href="https://docs.github.com/en/actions">GitHub Actions</a> open source plan</p></li>
</ul>
<p>The Bioconda logo is a derivative mark of Anaconda <sup>®</sup>, a trademark of
Anaconda, Inc registered in the U.S. and other countries. Anaconda, Inc. grants
permission of the derivative use but is not associated with Bioconda.</p>
<section id="citing-bioconda">
<h2>Citing Bioconda<a class="headerlink" href="#citing-bioconda" title="Link to this heading">¶</a></h2>
<p>When using Bioconda please <strong>cite our article</strong>:</p>
<blockquote>
<div><p>Grüning, Björn, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian
Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, the Bioconda
Team, and Johannes Köster. 2018. <em>Bioconda: Sustainable and
Comprehensive Software Distribution for the Life Sciences</em>. Nature
Methods, 2018 doi:<a class="extlink-doi reference external" href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a>.</p>
</div></blockquote>
</section>
<section id="id2">
<h2>Contributors<a class="headerlink" href="#id2" title="Link to this heading">¶</a></h2>
<section id="core">
<h3>Core<a class="headerlink" href="#core" title="Link to this heading">¶</a></h3>
<ul class="simple">
<li><p><a class="reference external" href="https://github.com/johanneskoester">Johannes Köster</a></p></li>
<li><p><a class="reference external" href="https://github.com/daler">Ryan Dale</a></p></li>
<li><p><a class="reference external" href="https://github.com/chapmanb">Brad Chapman</a></p></li>
<li><p><a class="reference external" href="https://github.com/tomkinsc">Chris Tomkins-Tinch</a></p></li>
<li><p><a class="reference external" href="https://github.com/bgruening">Björn Grüning</a></p></li>
<li><p><a class="reference external" href="https://github.com/druvus">Andreas Sjödin</a></p></li>
<li><p><a class="reference external" href="https://github.com/dpryan79">Devon Ryan</a></p></li>
<li><p><a class="reference external" href="https://github.com/epruesse">Elmar Pruesse</a></p></li>
<li><p><a class="reference external" href="https://github.com/rpetit3">Robert A. Petit III</a></p></li>
<li><p><a class="reference external" href="https://github.com/cbrueffer">Christian Brueffer</a></p></li>
<li><p><a class="reference external" href="https://github.com/aliciaaevans">Alicia Evans</a></p></li>
</ul>
</section>
<section id="former-core-members">
<h3>Former core members<a class="headerlink" href="#former-core-members" title="Link to this heading">¶</a></h3>
<ul class="simple">
<li><p><a class="reference external" href="https://github.com/jerowe">Jillian Rowe</a></p></li>
<li><p><a class="reference external" href="https://github.com/mbargull">Marcel Bargull</a></p></li>
<li><p><a class="reference external" href="https://github.com/rvalieris">Renan Valieris</a></p></li>
</ul>
</section>
<section id="team">
<h3>Team<a class="headerlink" href="#team" title="Link to this heading">¶</a></h3>
<p>Bioconda would not exist without the continuous hard work and support of the
wonderful community which includes over 1800 (as of 2023) <a class="reference external" href="https://github.com/bioconda/bioconda-recipes/graphs/contributors">contributors</a>.</p>
</section>
</section>
</section>
<section id="table-of-contents">
<h1>Table of contents<a class="headerlink" href="#table-of-contents" title="Link to this heading">¶</a></h1>
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