Merge branch 'main' into story1_divide-by-levels

.gitignore

@@ -2,4 +2,7 @@ _site
 .DS_Store
 *.swp
 .sass-cache
-__pycache__
+__pycache__
+node_modules
+videos
+.jekyll-cache

Makefile

@@ -37,57 +37,16 @@ create-env: ## create conda environment
 ACTIVATE_ENV = source $(dir ${CONDA})activate ${CONDA_ENV}
 install: clean ## install dependencies
 	$(ACTIVATE_ENV) && \
+		npm install && \
 		gem install bundler && \
 		bundle install
 .PHONY: install
 
 serve: ## run a local server
 	$(ACTIVATE_ENV) && \
-		bundle exec jekyll serve
+		bundle exec jekyll serve --strict_front_matter -d _site/DNAnalyzer -P ${PORT} -H ${PDF_HOST} ${FLAGS}
 .PHONY: serve
 
-detached-serve: ## run a local server in detached mode
-	$(ACTIVATE_ENV) && \
-		bundle exec jekyll serve --detach -P ${PORT} -H ${PDF_HOST} ${FLAGS}
-.PHONY: detached-serve
-
-pdf: detached-serve ## generate the PDF of the protocols
-	mkdir -p $(PDF_DIR)
-	@for t in $(PROTOCOLS); do \
-		name="$(PDF_DIR)/$$(echo $$t | tr '/' '-' | sed -e 's/.html/-instructors.pdf/' -e 's/^-//' -e 's/-index//')"; \
-		${CHROME} \
-            --headless \
-            --disable-gpu \
-            --print-to-pdf="$$name" \
-            "$(SITE_URL)/protocols/$$t" \
-            2> /dev/null ; \
-		name="$(PDF_DIR)/$$(echo $$t | tr '/' '-' | sed -e 's/.html/-learners.pdf/' -e 's/^-//' -e 's/-index//')"; \
-		${CHROME} \
-            --headless \
-            --disable-gpu \
-            --print-to-pdf="$$name" \
-            "$(SITE_URL)/protocols/$$t?without-details" \
-            2> /dev/null ; \
-	done
-
-	${CHROME} \
-		--headless \
-		--disable-gpu \
-		--print-to-pdf="$(PDF_DIR)/beer-dna-sequencing-flongle-instructor.pdf" \
-		"$(SITE_URL)/protocols/beer-dna-sequencing?flongle" \
-		2> /dev/null
-
-	${CHROME} \
-		--headless \
-		--disable-gpu \
-		--print-to-pdf="$(PDF_DIR)/beer-dna-sequencing-flongle-learners.pdf" \
-		"$(SITE_URL)/protocols/beer-dna-sequencing?flongle?without-details" \
-		2> /dev/null
-
-
-	pkill -f jekyll
-.PHONY: pdf
-
 help:
 	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
 .PHONY: help

README.md

@@ -108,3 +108,34 @@ In the sequel, we assume you use miniconda.
 
 7. Open the website in your favorite browser at:
    [http://127.0.0.1:4000/](http://127.0.0.1:4000/)
+
+
+
+## Generate videos
+
+### Requirements
+
+Ubuntu
+
+```
+$ sudo apt-get install sox
+$ sudo apt-get install libsox-fmt-mp3
+```
+
+#### Steps
+
+In different terminals:
+
+1. Run website 
+1. Launch MozillaTTS for speech
+
+   ```
+   $ docker run -it -p 5002:5002 synesthesiam/mozillatts
+   ```
+
+2. Launch scripts
+
+   ```
+   $ conda activate dnanalyzer
+   $ ./bin/ari-make.sh <path to slide>
+   ```

_config.yml

@@ -2,6 +2,7 @@
 title: DNAnalyzer
 description: >
   An online & interactive game on DNA data analysis!
+url: "https://streetscience.community"
 baseurl: "/DNAnalyzer"
 
 # Social

_includes/default-header.html

@@ -4,7 +4,6 @@
 
       <a class="navbar-item" href="{{ site.baseurl }}/">
           <img src="{{ site.baseurl }}/images/logo.png" alt="DNAnalyzer">
-
       </a>
 
       <a

about.md

@@ -75,4 +75,4 @@ we ask that you follow our [code of conduct]({{ site.github.repository_url
 
 Funding
 - [University of Freiburg](https://uni-freiburg.de/)
-- [de.NBI](https://www.denbi.de/), the German Network for Bioinformatics Infrastructure, for the MinION
+- [de.NBI](https://www.denbi.de/)

bin/ari-extract-script.rb

@@ -0,0 +1,135 @@
+### Script adapted from Galaxy Training Network script
+### https://github.com/galaxyproject/training-material/
+
+#!/usr/bin/env ruby
+require 'yaml'
+require 'shellwords'
+require 'json'
+
+fn = ARGV[0]
+metadata = YAML.load_file(fn)
+
+ARI_MAP = File.expand_path(File.join(__dir__, 'ari-map.yml'))
+WORD_MAP = {}
+YAML.load_file(ARI_MAP).each_pair do |k,v|
+ WORD_MAP.merge!({k.downcase => v})
+end
+
+APPROVED_VOICES = {
+  "en" => [
+    {"id" =>"Amy"     , "lang" => "en-GB" , "neural" => true},
+    {"id" =>"Aria"    , "lang" => "en-NZ" , "neural" => true},
+    {"id" =>"Brian"   , "lang" => "en-GB" , "neural" => true},
+    {"id" =>"Emma"    , "lang" => "en-GB" , "neural" => true},
+    {"id" =>"Joanna"  , "lang" => "en-US" , "neural" => true},
+    {"id" =>"Joey"    , "lang" => "en-US" , "neural" => true},
+    {"id" =>"Kendra"  , "lang" => "en-US" , "neural" => true},
+    {"id" =>"Matthew" , "lang" => "en-US" , "neural" => true},
+    {"id" =>"Nicole"  , "lang" => "en-AU" , "neural" => false},
+    {"id" =>"Olivia"  , "lang" => "en-AU" , "neural" => true},
+    {"id" =>"Raveena" , "lang" => "en-IN" , "neural" => false},
+    {"id" =>"Salli"   , "lang" => "en-US" , "neural" => true}
+  ],
+  "es" => [
+    { "id" => "Miguel"   , "lang" => "es-US" , "neural" => false },
+    { "id" => "Mia"      , "lang" => "es-MX" , "neural" => false },
+    { "id" => "Enrique"  , "lang" => "es-ES" , "neural" => false },
+    { "id" => "Conchita" , "lang" => "es-ES" , "neural" => false },
+    { "id" => "Lupe"     , "lang" => "es-US" , "neural" => true }
+  ]
+}
+
+m_lang = metadata.fetch('lang', 'en')
+m_voice = metadata.fetch('voice', nil)
+
+# Parse the material for the slide notes
+file = File.open(fn)
+lines = file.readlines.map(&:chomp)
+
+# The structure will be
+# ---
+# meta
+# ---
+#
+# contents
+
+# +1 because we skipped the 0th entry, +1 again to not include the `---`
+end_meta = lines[1..-1].index("---") + 2
+
+# Strip off the metadata
+contents = lines[end_meta..-1]
+
+# This will be our final script
+blocks = [[metadata['title']]]
+
+
+# Accumulate portions between ??? and ---
+current_block = []
+in_notes = false
+contents.each{ |x|
+  # Check whether we're in the notes or out of them.
+  if x == "???" then
+    in_notes = true
+  elsif x == "---" or x == "--" then
+    if in_notes then
+      blocks.push(current_block)
+      current_block = []
+    end
+
+    in_notes = false
+  end
+
+  if in_notes then
+    current_block.push(x)
+  end
+}
+blocks.push(current_block)
+
+if m_lang == "en" then
+  blocks.push(["Thank you for watching!"])
+elsif m_lang == "es" then
+  blocks.push(["¡Gracias por ver este vídeo!"])
+else
+  blocks.push(["Thank you for watching!"])
+end
+
+# For each block, cleanup first.
+blocks = blocks.map{ |block|
+  # Remove the - prefix from each line
+  script_lines = block.map{ |x| x.strip.delete_prefix("- ") }
+  # Remove the leading ???
+  if script_lines[0] == '???'
+    script_lines = script_lines[1..-1]
+  end
+  # Remove blank entries
+  script_lines = script_lines.select{ |x| x.length != 0 }
+  script_lines = script_lines.map{ |line|
+    line.delete_prefix("- ")
+    line.gsub!(/`/, '"')
+    # If they don't end with punctuation, fix it.
+    if ! (line.end_with?('.') or line.end_with?('?') or line.end_with?('!'))
+      line += '.'
+    end
+
+    line
+  }
+  script_lines
+}
+
+#out_subs.write(blocks.map{ |line| line.join(" ") }.join("\n"))
+res = Hash.new
+res["blocks"] = blocks
+
+if m_voice.nil? then
+  if m_lang == "en" then
+    res["voice"] = APPROVED_VOICES['en'].sample
+  elsif m_lang == "es" then
+    res["voice"] = APPROVED_VOICES['es'].sample
+  else
+    res["voice"] = APPROVED_VOICES['en'].sample
+  end
+else
+  res["voice"] = metadata['voice']
+end
+
+print JSON.pretty_generate(res)

bin/ari-make.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+### Script adapted from Galaxy Training Network script
+### https://github.com/galaxyproject/training-material/
+
+set -e
+
+function cleanup(){
+	kill $(pgrep -f $(npm bin)/http-server) || true
+}
+
+trap cleanup EXIT
+
+slides=$1
+echo "====== $slides ======"
+dir="$(dirname "$slides")"
+pdf="$dir/$(basename "$slides" .html).pdf"
+mp4="videos/$dir/$(basename "$slides" .html).mp4"
+built_slides="_site/$slides"
+
+# Launch small server
+$(npm bin)/http-server -p 9876 _site &
+
+# Process the slides
+echo $built_slides
+$(npm bin)/decktape automatic -s 1920x1080 http://localhost:9876/DNAnalyzer/$slides _site/DNAnalyzer/$pdf; \
+
+# Build the slides
+echo ari.sh "_site/DNAnalyzer/$pdf" "$slides" "$mp4"
+./bin/ari.sh "_site/DNAnalyzer/$pdf" "$slides" "$mp4"
+
+cleanup

bin/ari-map.yml

@@ -0,0 +1,61 @@
+---
+# These aren't needed, they're said correctly. Acronyms work fine.
+#CMVFS: C V M F S
+#IDC: I D C
+# However if the usage is ever lowercase, it'll attempt to pronounce it directly
+bwa: BWA
+# And for some you'll need to separate the letter part vs pronounced part
+BWA-MEM: BWA mem
+'usegalaxy.*': usegalaxy dot star
+gxadmin: GX admin
+nginx: engine X
+systemd: system D
+/etc: / E T C
+systemctl: system C T L
+cgroup: C group
+cgroups: C groups
+telegraf: telegraph
+sqlite: SQL light
+SQLAlchemy: SQL alchemy
+fastqc: fast QC
+ntpdate: NTP date
+RedHat: Red Hat
+ATAC-Seq: ATAC Seq
+Tn5: T N five
+paired-end: paired end
+# For some reason moz-tts doesn't pronounce right in a sentence unless it's
+# lowercase. This gives parity with AWS
+RAM: ram
+uWSGI: "you whiskey"
+GIL: gill
+DRMAA: drama
+hisat2: high sat 2
+Node.js: node JS
+db-skip-locked: DB skip locked
+REST: rest
+FASTQ: fast Q
+scRNA-seq: S C RNA seq
+scRNA: S C RNA
+RNAmmer: RNA mer
+Rfam: R fam
+Pfam: P fam
+m/z: MZ
+'>': greater than sign
+b-ions: B ions
+y-ions: Y ions
+MSstats: MS stats
+LC-MS/MS: LC MS MS
+topN: top N
+miRNA: micro RNA
+miRNAs: micro RNAs
+mRNA: m RNA
+mRNAs: m RNAs
+FastQC: fast QC
+MultiQC: multi QC
+DESeq2: D E Seq 2
+TargetFinder: target finder
+MiRDeep2: mir deep 2
+cutadapt: cut adapt
+b': b prime
+e': e prime
+/: forward slash