docs: update docs

bin/install_samtools.sh

@@ -1,7 +1,10 @@
 #!/bin/bash
 #
-#  Sets up PharmCAT in the current directory after checking for basic requirements.
+# Sets up samtools.
+# Requires the following libraries on Ubuntu: libbz2-dev, libncurses-dev, liblzma-dev.
 #
+# Can be called with a single parameter, defining where to install (will be supplied as --prefix to configure).
+# Defaults to current directory.
 #
 
 set -e

docs/About-Us.md

@@ -5,20 +5,18 @@ nav_order: 10
 ---
 # About Us
 
-## Co-PIs
+PharmCAT is developed and maintained by Mark Woon (lead developer), Ryan Whaley (lead developer),
+Katrin Sangkuhl (lead scientist) and Michelle Whirl-Carrillo (scientist) at Stanford University.
+Binglan Li developed the preprocessor.
 
-Teri Klein (Stanford University) and Marylyn Ritchie (University of Pennsylvania)
+The co-Principal Investigators on the project are Teri Klein at Stanford University and Marylyn Ritchie at University of
+Pennsylvania.
 
 
-## Current Team
+## Other Team Members
 
 | Name                    | Institution                |
 |:------------------------|:---------------------------|
-| Binglan Li              | Stanford University        |
-| Katrin Sangkuhl         | Stanford University        |
-| Ryan Whaley             | Stanford University        |
-| Michelle Whirl-Carrillo | Stanford University        |
-| Mark Woon               | Stanford University        |  
 | Karl Keat               | University of Pennsylvania |
 | Andre Rico              | University of Pennsylvania |
 | Sony Tuteja             | University of Pennsylvania |
@@ -43,6 +41,7 @@ PharmCAT is now part of [ClinPGx](https://clinpgx.org).  PharmCAT's scientific a
 | Mark Dunnenberger  | Northshore University Health System        |
 | Philip Empey       | University of Pittsburgh                   |
 | Alex Frase         | University of Pennsylvania                 |
+| Obed Garcia        | Stanford University                        |
 | Robert Freimuth    | Mayo Clinic                                |
 | Andrea Gaedigk     | Children's Mercy Hospital                  |
 | Adam Gordon        | University of Washington                   |

docs/FAQs.md

@@ -6,8 +6,14 @@ nav_order: 8
 # Frequently Asked Questions
 {: .no_toc }
 
+<details open markdown="block">
+  <summary>
+    Table of contents
+  </summary>
+  {: .text-delta }
 1. TOC
 {:toc}
+</details>
 
 ## General
 

docs/Genes-Drugs.md

@@ -45,7 +45,7 @@ These genes will not get allele matches from PharmCAT<sup>*</sup>. However, you
 matching recommendation data.
 
 See [Outside Call Format](/using/Outside-Call-Format) for formatting details and
-[Calling CYP2D6](/using/Calling-CYP2D6) or [Calling HLA](/using/Calling-HLA) for how to obtain CYP2D6 or
+[Calling CYP2D6](/using/Calling-CYP2D6) or [Calling HLA](/using/Calling-HLA) for how to get CYP2D6 or
 HLA calls, respectively, using sequencing data.
 
 | Gene | CPIC | DPWG |

docs/Makefile

@@ -18,3 +18,7 @@ next: clean build
 dev:
 	bundle exec just-the-docs rake search:init
 	bundle exec jekyll build --incremental
+	cd ..; yarn localDocs
+
+local:
+	bundle exec jekyll serve --force-polling --incremental

docs/_config.yml

@@ -30,7 +30,7 @@ mermaid:
 color_scheme: pharmcat
 ga_tracking: G-7ZP1HHBWTE
 ga_tracking_anonymize_ip: true
-logo: /images/pharmcat_header.png
+logo: /images/pharmcat_logo.svg
 show_downloads: true
 
 pharmcat_version: 2.15.5

docs/_sass/color_schemes/pharmcat.scss

@@ -3,8 +3,9 @@ $link-color: $blue-200;
 // from https://github.com/just-the-docs/just-the-docs/issues/171#issuecomment-538794741
 $callouts: (
     info: ($blue-300, rgba($blue-000, .2), 'INFO'),
-    warn: ($yellow-300, rgba($yellow-000, .2), 'WARNING'),
-    danger: ($red-300, rgba($red-000, .2), 'DANGER')
+    warn: ($yellow-300, rgba($yellow-000, .3), 'WARNING'),
+    danger: ($red-300, rgba($red-000, .2), 'DANGER'),
+    attention: ($yellow-300, rgba($yellow-000, .1), 'attention')
 );
 
 @each $class, $props in $callouts {
@@ -31,18 +32,29 @@ $callouts: (
 
 .logoDiv {
   display: flex;
+  margin-top: 1rem;
+  margin-bottom: 1rem;
+
+  &__logo {
+    height: 120px;
+    margin-right: 2rem;
+
+    img {
+      height: 120px;
+    }
+  }
 
   &__links {
     display: flex;
     flex-wrap: wrap;
     align-self: center;
-    margin-top: 8%;
+    margin-top: 4rem;
 
-    @media (max-width: 715px) {
-      margin-top: 5%;
+    @media (max-width: 630px) {
+      margin-top: 1rem;
     }
-    @media (min-width: 800px) and (max-width: 995px) {
-      margin-top: 5%;
+    @media (min-width: 800px) and (max-width: 915px) {
+      margin-top: 1rem;
     }
 
     span {
@@ -56,7 +68,29 @@ $callouts: (
   }
 }
 
+.img-translation {
+  max-width: 600px;
+
+  @media (max-width: 800px) {
+    max-width: 100%;
+  }
+}
+.img-pipeline {
+  margin-top: 1rem;
+}
+
+.language-plaintext, .language-console {
+  line-height: 1;
+  code {
+    line-height: 1;
+  }
+}
+
 // hide footer so that menu works on mobile
 .site-footer {
   display: none;
 }
+
+.site-logo {
+  height: 3.2rem !important;
+}

docs/examples/index.md

@@ -25,22 +25,22 @@ This is an example of an optional file of [outside diplotype calls](/using/Outsi
 
 ### Named Allele Matcher output
 
-The `Named Allele Matcher` component generates both HTML and JSON files with detailed information about how data in the 
+The `Named Allele Matcher` module generates both HTML and JSON files with detailed information about how data in the 
 sample VCF matches up with haplotype definitions.
 
 - [example matcher HTML](pharmcat.example.match.html)
 - [example matcher JSON](pharmcat.example.match.json)
 
 ### Phenotyper output
 
-The `Phenotyper` component takes data from the `Named Allele Matcher` and combines it with outside call data to assign 
+The `Phenotyper` module takes data from the `Named Allele Matcher` and combines it with outside call data to assign 
 function and metabolizer values.
 
 - [example phenotype JSON](pharmcat.example.phenotype.json)
 
 ### Reporter output
 
-The `Reporter` component takes data from the `Phenotyper` and matches phenotypes to information found in CPIC guideline
+The `Reporter` module takes data from the `Phenotyper` and matches phenotypes to information found in CPIC guideline
 data. This data is visible in an HTML report and also in a JSON file for machine parsing.
 
 - [example report HTML](pharmcat.example.report.html)