Deploying to gh-pages from @ f47e2be 🚀

vanheeringen-lab · Feb 3, 2024 · 3d3522a · 3d3522a
1 parent 7ee8f5e
commit 3d3522a
Show file tree

Hide file tree

Showing 64 changed files with 646 additions and 584 deletions.
diff --git a/.doctrees/CONTRIBUTING.doctree b/.doctrees/CONTRIBUTING.doctree
diff --git a/.doctrees/content/CHANGELOG.doctree b/.doctrees/content/CHANGELOG.doctree
diff --git a/.doctrees/content/DESeq2.doctree b/.doctrees/content/DESeq2.doctree
diff --git a/.doctrees/content/all_rules.doctree b/.doctrees/content/all_rules.doctree
diff --git a/.doctrees/content/cli.doctree b/.doctrees/content/cli.doctree
diff --git a/.doctrees/content/extensive_docs.doctree b/.doctrees/content/extensive_docs.doctree
diff --git a/.doctrees/content/extracontent.doctree b/.doctrees/content/extracontent.doctree
diff --git a/.doctrees/content/faq.doctree b/.doctrees/content/faq.doctree
diff --git a/.doctrees/content/gettingstarted.doctree b/.doctrees/content/gettingstarted.doctree
diff --git a/.doctrees/content/multiqc.doctree b/.doctrees/content/multiqc.doctree
diff --git a/.doctrees/content/results.doctree b/.doctrees/content/results.doctree
diff --git a/.doctrees/content/scATAC_postprocessing.doctree b/.doctrees/content/scATAC_postprocessing.doctree
diff --git a/.doctrees/content/schemas.doctree b/.doctrees/content/schemas.doctree
diff --git a/.doctrees/content/seq2science_profiles.doctree b/.doctrees/content/seq2science_profiles.doctree
diff --git a/.doctrees/content/workflows.doctree b/.doctrees/content/workflows.doctree
diff --git a/.doctrees/content/workflows/alignment.doctree b/.doctrees/content/workflows/alignment.doctree
diff --git a/.doctrees/content/workflows/atac_seq.doctree b/.doctrees/content/workflows/atac_seq.doctree
diff --git a/.doctrees/content/workflows/chip_seq.doctree b/.doctrees/content/workflows/chip_seq.doctree
diff --git a/.doctrees/content/workflows/download_fastq.doctree b/.doctrees/content/workflows/download_fastq.doctree
diff --git a/.doctrees/content/workflows/rna_seq.doctree b/.doctrees/content/workflows/rna_seq.doctree
diff --git a/.doctrees/content/workflows/scatac_seq.doctree b/.doctrees/content/workflows/scatac_seq.doctree
diff --git a/.doctrees/content/workflows/scrna_seq.doctree b/.doctrees/content/workflows/scrna_seq.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Contributing to seq2science &mdash; seq2science  documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->

diff --git a/_sources/content/CHANGELOG.md.txt b/_sources/content/CHANGELOG.md.txt
@@ -9,6 +9,12 @@ All changed fall under either one of these types: `Added`, `Changed`, `Deprecate
 
 ## [Unreleased]
 
+### Fixed
+
+- chipseeker env got corrupted, it should work again.
+- replaced deprecated --split-e flag with --split-3 flag for fastq downloading
+- removed support for GSA as their "API" changed
+
 ## [1.2.1] - 2023-11-15
 
 ### Fixed

diff --git a/_sources/content/all_rules.md.txt b/_sources/content/all_rules.md.txt
diff --git a/_sources/content/workflows/download_fastq.md.txt b/_sources/content/workflows/download_fastq.md.txt
@@ -9,7 +9,7 @@ Downloading public data in bulk from the NCBI, ENA, and DDBJ databases has never
 
 #### Download SRA file
 
-The five most popular databases that store sequencing data are National Center for Biotechnology Information (NCBI), the European Nucleotide Archive (ENA), the DNA Data Bank of Japan (DDBJ), the Genome Sequence Archive (GSA), and the Encode project (ENCODE).
+The five most popular databases that store sequencing data are National Center for Biotechnology Information (NCBI), the European Nucleotide Archive (ENA), the DNA Data Bank of Japan (DDBJ), the Genome Sequence Archive (GSA) (GSA is currently not supported anymore), and the Encode project (ENCODE).
 ENA, ENCODE, and GSA store the actual fastq files, and DDBJ and NCBI store the raw data (as a sra file) from which a fastq can be derived.
 For this reason for each sample on DDBJ and NCBI seq2science will first check if it can be downloaded from ENA as a fastq directly.
 Otherwise we will download the samples in its raw format. To convert this data to a fastq it has to be "*dumped*".
@@ -22,7 +22,6 @@ As an example, the `samples.tsv` could look something like this:
 
 ```
 sample
-CRX123    <-- GSA experiment
 DRX890    <-- DDBJ experiment
 DRR098    <-- DDBJ run
 ENCSR765  <-- ENCODE assay

diff --git a/_static/alignment.png b/_static/alignment.png
diff --git a/_static/atac_seq.png b/_static/atac_seq.png
diff --git a/_static/chip_seq.png b/_static/chip_seq.png
diff --git a/_static/download_fastq.png b/_static/download_fastq.png
diff --git a/_static/rna_seq.png b/_static/rna_seq.png
diff --git a/_static/scatac_seq.png b/_static/scatac_seq.png
diff --git a/_static/scrna_seq.png b/_static/scrna_seq.png
diff --git a/content/CHANGELOG.html b/content/CHANGELOG.html
diff --git a/content/DESeq2.html b/content/DESeq2.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Differential gene/peak analysis &mdash; seq2science  documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->

diff --git a/content/all_rules.html b/content/all_rules.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Per rule explanation &mdash; seq2science  documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -647,15 +649,15 @@ <h2>featureCounts<a class="headerlink" href="#featurecounts" title="Link to this
 mv $(dirname {output.real_out})/$(basename {output.summary}) {output.summary}
 </pre></div>
 </div>
-<p><a class="reference external" href="https://github.com/vanheeringen-lab/seq2science/blob/docs_updates/seq2science/envs/gene_counts.yaml">featureCounts environment</a>.</p>
+<p><a class="reference external" href="https://github.com/vanheeringen-lab/seq2science/blob/docs_updates/seq2science/envs/subread.yaml">featureCounts environment</a>.</p>
 </section>
 <section id="id1">
 <h2>featurecounts<a class="headerlink" href="#id1" title="Link to this heading"></a></h2>
 <p>summarize reads to gene level. Outputs a counts table per bam file.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">featureCounts</span> <span class="o">-</span><span class="n">a</span> <span class="p">{</span><span class="nb">input</span><span class="o">.</span><span class="n">gtf</span><span class="p">}</span> <span class="p">{</span><span class="nb">input</span><span class="o">.</span><span class="n">bam</span><span class="p">}</span> <span class="p">{</span><span class="n">params</span><span class="o">.</span><span class="n">endedness</span><span class="p">}</span> <span class="o">-</span><span class="n">s</span> <span class="p">{</span><span class="n">params</span><span class="o">.</span><span class="n">strandedness</span><span class="p">}</span> <span class="p">{</span><span class="n">params</span><span class="o">.</span><span class="n">user_flags</span><span class="p">}</span> <span class="o">-</span><span class="n">T</span> <span class="p">{</span><span class="n">threads</span><span class="p">}</span> <span class="o">-</span><span class="n">o</span> <span class="p">{</span><span class="n">output</span><span class="p">}</span> <span class="o">&gt;</span> <span class="p">{</span><span class="n">log</span><span class="p">}</span> <span class="mi">2</span><span class="o">&gt;&amp;</span><span class="mi">1</span>
 </pre></div>
 </div>
-<p><a class="reference external" href="https://github.com/vanheeringen-lab/seq2science/blob/docs_updates/seq2science/envs/gene_counts.yaml">featurecounts environment</a>.</p>
+<p><a class="reference external" href="https://github.com/vanheeringen-lab/seq2science/blob/docs_updates/seq2science/envs/subread.yaml">featurecounts environment</a>.</p>
 </section>
 <section id="full-decoy-transcripts">
 <h2>full_decoy_transcripts<a class="headerlink" href="#full-decoy-transcripts" title="Link to this heading"></a></h2>
@@ -1407,7 +1409,7 @@ <h2>sra2fastq_PE<a class="headerlink" href="#sra2fastq-pe" title="Link to this h
 
 # dump to tmp dir
 parallel-fastq-dump -s {input} -O {output.tmpdir} \
---threads {threads} --split-e --skip-technical --dumpbase \
+--threads {threads} --split-3 --skip-technical --dumpbase \
 --readids --clip --read-filter pass --defline-seq &#39;@$ac.$si.$sg/$ri&#39; \
 --defline-qual &#39;+&#39; --gzip &gt;&gt; {log} 2&gt;&amp;1
 

diff --git a/content/cli.html b/content/cli.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Command line interface &mdash; seq2science  documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -106,7 +108,7 @@
 <h1>Command line interface<a class="headerlink" href="#command-line-interface" title="Link to this heading"></a></h1>
 <section id="init">
 <h2>init<a class="headerlink" href="#init" title="Link to this heading"></a></h2>
-<p><p>Each workflow requires a configuration and samples file to run. Running “seq2science init {workflow}” initialises a default configuration and samples file for the specific workflow. Supported workflows: alignment, download-fastq, scrna-seq, atac-seq, scatac-seq, chip-seq, rna-seq</p>
+<p><p>Each workflow requires a configuration and samples file to run. Running “seq2science init {workflow}” initialises a default configuration and samples file for the specific workflow. Supported workflows: alignment, scrna-seq, scatac-seq, atac-seq, rna-seq, download-fastq, chip-seq</p>
 </p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">seq2science</span> <span class="n">init</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="nb">dir</span> <span class="n">PATH</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">f</span><span class="p">]</span> <span class="n">WORKFLOW</span>
 </pre></div>
@@ -115,7 +117,7 @@ <h2>init<a class="headerlink" href="#init" title="Link to this heading"></a><
 <h3>Positional Arguments<a class="headerlink" href="#positional-arguments" title="Link to this heading"></a></h3>
 <dl class="option-list">
 <dt><kbd>WORKFLOW</kbd></dt>
-<dd><p>Possible choices: alignment, download-fastq, scrna-seq, atac-seq, scatac-seq, chip-seq, rna-seq</p>
+<dd><p>Possible choices: alignment, scrna-seq, scatac-seq, atac-seq, rna-seq, download-fastq, chip-seq</p>
 </dd>
 </dl>
 </section>
@@ -136,7 +138,7 @@ <h3>Named Arguments<a class="headerlink" href="#named-arguments" title="Link to
 <hr class="docutils" />
 <section id="run">
 <h2>run<a class="headerlink" href="#run" title="Link to this heading"></a></h2>
-<p><p>Run a complete workflow. This requires that a config and samples file are either present in the current directory, or passed as an argument. Supported workflows: alignment, download-fastq, scrna-seq, atac-seq, scatac-seq, chip-seq, rna-seq</p>
+<p><p>Run a complete workflow. This requires that a config and samples file are either present in the current directory, or passed as an argument. Supported workflows: alignment, scrna-seq, scatac-seq, atac-seq, rna-seq, download-fastq, chip-seq</p>
 </p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">seq2science</span> <span class="n">run</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">j</span> <span class="n">N</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">n</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">r</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">skip</span><span class="o">-</span><span class="n">rerun</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">k</span><span class="p">]</span>
                        <span class="p">[</span><span class="o">--</span><span class="n">rerun</span><span class="o">-</span><span class="n">incomplete</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">unlock</span><span class="p">]</span>
@@ -150,7 +152,7 @@ <h2>run<a class="headerlink" href="#run" title="Link to this heading"></a></h
 <h3>Positional Arguments<a class="headerlink" href="#positional-arguments" title="Link to this heading"></a></h3>
 <dl class="option-list">
 <dt><kbd>WORKFLOW</kbd></dt>
-<dd><p>Possible choices: alignment, download-fastq, scrna-seq, atac-seq, scatac-seq, chip-seq, rna-seq</p>
+<dd><p>Possible choices: alignment, scrna-seq, scatac-seq, atac-seq, rna-seq, download-fastq, chip-seq</p>
 </dd>
 </dl>
 </section>
@@ -217,7 +219,7 @@ <h2>clean<a class="headerlink" href="#clean" title="Link to this heading"></a
 <hr class="docutils" />
 <section id="explain">
 <h2>explain<a class="headerlink" href="#explain" title="Link to this heading"></a></h2>
-<p><p>Explains what has/will be done for the workflow. This prints a string which can serve as a skeleton for your material &amp; methods section. Supported workflows: alignment, download-fastq, scrna-seq, atac-seq, scatac-seq, chip-seq, rna-seq</p>
+<p><p>Explains what has/will be done for the workflow. This prints a string which can serve as a skeleton for your material &amp; methods section. Supported workflows: alignment, scrna-seq, scatac-seq, atac-seq, rna-seq, download-fastq, chip-seq</p>
 </p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">seq2science</span> <span class="n">explain</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">hyperref</span><span class="p">]</span>
                            <span class="p">[</span><span class="o">--</span><span class="n">snakemakeOptions</span> <span class="n">KEY</span><span class="o">=</span><span class="n">VAL</span> <span class="p">[</span><span class="n">KEY</span><span class="o">=</span><span class="n">VAL</span> <span class="o">...</span><span class="p">]]</span>
@@ -229,7 +231,7 @@ <h2>explain<a class="headerlink" href="#explain" title="Link to this heading">
 <h3>Positional Arguments<a class="headerlink" href="#positional-arguments" title="Link to this heading"></a></h3>
 <dl class="option-list">
 <dt><kbd>WORKFLOW</kbd></dt>
-<dd><p>Possible choices: alignment, download-fastq, scrna-seq, atac-seq, scatac-seq, chip-seq, rna-seq</p>
+<dd><p>Possible choices: alignment, scrna-seq, scatac-seq, atac-seq, rna-seq, download-fastq, chip-seq</p>
 </dd>
 </dl>
 </section>

diff --git a/content/extensive_docs.html b/content/extensive_docs.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Extensive docs &mdash; seq2science  documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->

diff --git a/content/extracontent.html b/content/extracontent.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Extra resources &mdash; seq2science  documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->

diff --git a/content/faq.html b/content/faq.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Frequently Asked Questions (FAQ) &mdash; seq2science  documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->

diff --git a/content/gettingstarted.html b/content/gettingstarted.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Getting started &mdash; seq2science  documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->

diff --git a/content/multiqc.html b/content/multiqc.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Example MultiQC report &mdash; seq2science  documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+
+
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->