Add scientific references section

Add papers and licenses sections. Add footer links. Add AODP mention in landing page.

assets/sass/footer.sass

@@ -8,5 +8,18 @@
   padding: 2rem
   justify-content: space-between
 
-  +landscape
+  ul
     display: flex
+    list-style-type: none
+    padding: 0
+
+    & > li
+      padding: 0 5px
+
+    &.footer-link-list > li
+      padding: 0
+
+      &:not(:last-child):after
+        content: "|"
+        padding: 0 5px 0 3px
+

assets/sass/literature-reference.sass

@@ -0,0 +1,4 @@
+p.literature-reference
+    padding-left: 30px
+    text-indent: -15px
+

assets/style.sass

@@ -20,6 +20,7 @@
 @import "sass/icon"
 @import "sass/image"
 @import "sass/landing"
+@import "sass/literature-reference"
 @import "sass/nav"
 @import "sass/notes"
 @import "sass/options"

config.toml

@@ -31,6 +31,10 @@ pygmentsCodeFences = true
     name = "Science"
     weight = 40
 
+  [[menu.manual]]
+    name = "Sources"
+    weight = 50
+
   [[menu.developer]]
     name = "Contributing"
     weight = 10

content/docs/manual/science/references/index.md

@@ -0,0 +1,8 @@
+---
+title: "References"
+description: "See references to work that made Virtool possible."
+menu:
+  manual:
+    parent: "Science"
+    weight: 30
+---

content/docs/manual/sources/licenses/index.md

@@ -0,0 +1,9 @@
+---
+title: "Licenses"
+description: "Licenses for Virtool's software dependencies."
+menu:
+    manual:
+        parent: "Sources"
+---
+
+There is nothing here yet.

content/docs/manual/sources/papers/index.md

@@ -0,0 +1,104 @@
+---
+title: "Papers"
+description: "Literature references for scientific work that made Virtool possible."
+menu:
+    manual:
+        parent: "Sources"
+---
+
+# References
+
+## AODP
+
+AODP is used to run barcode reference building and sample analysis in Virtool. It was integrated into Virtool through a joint project with its Developer, Wen Chen.
+
+{{< reference 
+    authors="Zahariev M, Chen W, Visagie CM & Lévesque CA"
+    year="2018"
+    title="Cluster oligonucleotide signatures for rapid identification by sequencing"
+    journal="BMC Bioinformatics"
+    issue="19"
+    doi="10.1186/s12859-018-2363-3"
+>}}
+
+<small><strong></strong><small>
+
+## Bowtie2
+
+Bowtie2 is used to map reads to known viral and subtraction genomes.
+
+{{< reference 
+    authors="Langmead B & Salzberg SL"
+    year="2012"
+    title="Fast gapped-read alignment with Bowtie 2"
+    journal="Nat Methods"
+    issue="9"
+    doi="10.1038/nmeth.1923"
+>}}
+
+## FLASH
+
+FLASH is used to join overlapping paired-end reads during barcode analysis using AODP.
+
+
+{{< reference 
+    authors="Magoč T & Salzberg SL"
+    year="2011"
+    title="FLASH: fast length adjustment of short reads to improve genome assemblies"
+    journal="Bioinformatics"
+    issue="27"
+    doi="10.1093/bioinformatics/btr507"
+>}}
+
+## HMMER
+
+HMMER is used to predict viral protein motifs in the NuVs novel virus discovery workflow.
+
+{{< reference 
+    authors="Eddy SR"
+    year="2011"
+    title="Fast gapped-read alignment with Bowtie 2"
+    journal="PLoS Comput Biol"
+    issue="7"
+    doi="10.1371/journal.pcbi.1002195"
+>}}
+
+## Pathoscope
+
+A modified version of the Pathoscope2 strain identification framework is used to detect known viruses.
+
+{{< reference 
+    authors="Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA & Johnson WE"
+    year="2014"
+    title="PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples"
+    journal="Microbiome"
+    issue="2"
+    doi="10.1186/2049-2618-2-33"
+>}}
+
+
+## Skewer
+
+Skewer is used to trim sample reads.
+
+{{< reference
+    authors="Jiang H, Lei R, Ding S-W & Zhu S"
+    year="2014"
+    title="Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads"
+    journal="BMC Bioinformatics"
+    issue="15"
+    doi="10.1186/1471-2105-15-182"
+>}}
+
+## SPAdes
+
+SPAdes is used to assemble contigs in the NuVs novel virus discovery workflow.
+
+{{< reference
+    authors="Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VW, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, & Pevzner PA"
+    year="2012"
+    title="SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing"
+    journal="J Comput Biol"
+    issue="19"
+    doi="10.1089/cmb.2012.0021"
+>}}

layouts/_default/baseof.html

@@ -46,10 +46,34 @@
   </div>
 
   <footer class="footer">
-    <div class="copyright">
-    </div>
-    <div class="license">
-      Licensed under <a href="https://github.com/virtool/virtool/blob/master/LICENSE">MIT License</a>
+    <div class="container">
+      <ul>
+        <li>
+          <a title="Gitter Chat" href="https://gitter.im/virtool/virtool">
+            <span class="icon">
+              <i class="fab fa-gitter fa-lg"></i>
+            </span>
+          </a>
+        </li>
+        <li>
+          <a title="GitHub" href="https://github.com/virtool/virtool">
+            <span class="icon">
+              <i class="fab fa-github fa-lg"></i>
+            </span>
+          </a>
+        </li>
+      </ul>
+      <ul class="footer-link-list">
+        <li>
+          Licensed under <a href="https://github.com/virtool/virtool/blob/master/LICENSE">MIT License</a>
+        </li>
+        <li>
+          <a href="/docs/manual/sources/papers">Literature References</a>
+        </li>
+        <li>
+          <a href="/docs/manual/sources/licenses">Licenses</a>
+        </li>
+      </ul>
     </div>
   </footer>
 

layouts/index.html

@@ -75,7 +75,7 @@ <h2>
           Detect Novel Pathogens
         </h2>
         <p>
-          Use our assembly and profile hidden Markov model workflow to predict novel viral sequences
+          Use our assembly and profile hidden Markov model workflow to predict novel viral sequences.
         </p>
       </div>
       <div>
@@ -91,7 +91,7 @@ <h2>
           Sample Management
         </h2>
         <p>
-          Intuitively manage samples and their analyses
+          Intuitively manage samples and their analyses.
         </p>
       </div>
       <div>
@@ -107,7 +107,7 @@ <h2>
           QC
         </h2>
         <p>
-          Automatically run and view FastQC-based quality control (QC) on sample data
+          Automatically run and view FastQC-based quality control (QC) on sample data.
         </p>
       </div>
       <div>
@@ -123,7 +123,7 @@ <h2>
           Sequence References
         </h2>
         <p>
-          Construct collections of sequences organized into organization taxonomic units (OTU)</li>
+          Construct collections of sequences organized into organization taxonomic units (OTU).
         </p>
       </div>
       <div class="feature-side">
@@ -179,6 +179,22 @@ <h2>
         <img src="/images/subtraction.png" />
       </div>
     </div>
+
+    {{ partial "wave.html" . }}
+
+    <div class="feature">
+      <div>
+        <h2>
+          Open Source
+        </h2>
+        <p>
+          Virtool is open source and makes heavy use of <a href="/docs/manual/sources/licenses">open source software</a> and <a href="/docs/manual/sources/papers">published bioinformatic tools</a>.
+        </p>
+      </div>
+      <div>
+        <img src="/images/papers.png" />
+      </div>
+    </div>
   </div>
 </div>
 {{ end }}

layouts/shortcodes/reference.html

@@ -0,0 +1,5 @@
+{{ $doi := .Get "doi" }}
+
+<p class="box literature-reference">
+    <strong>{{ .Get "authors" }}</strong>. {{ .Get "year" }}. {{ .Get "title" }}. {{ .Get "journal"}}: {{ .Get "issue" }}. doi: <a href="https://doi.org/{{ $doi }}">{{ $doi }}</a>.
+</p>