Fixes

Makefile

@@ -8,6 +8,7 @@ SITE_URL=http://${PDF_HOST}:${PORT}
 PROTOCOLS=$(shell find _site/protocols/ -name 'index.html' | sed 's/_site\/protocols\///')
 
 CONDA = $(shell which conda)
+CONDA_ENV_DIR=$(shell dirname $(dir $(CONDA)))
 ifeq ($(CONDA),)
 	CONDA=${HOME}/miniconda3/bin/conda
 endif
@@ -39,6 +40,9 @@ install: clean ## install dependencies
 	$(ACTIVATE_ENV) && \
 		npm install && \
 		gem install bundler && \
+		pushd ${CONDA_ENV_DIR}/envs/${CONDA_ENV}/share/rubygems/bin && \
+		ln -sf ../../../bin/ruby ruby && \
+		popd && \
 		bundle install
 .PHONY: install
 

README.md

@@ -26,16 +26,16 @@ Technologies like DNA sequencing are getting cheaper and therefore more accessib
 
 ### The solution
 
-We are implementing an encouraging and easy-to-understand online game on DNA data analysis, the DNAnalyzer. 
+We are implementing an encouraging and easy-to-understand online game on DNA data analysis, the DNAnalyzer.
 
 We have some interesting story, to make the game more exciting. You can see them [here](stories/README.md)
 
-The game, implemented in Galaxy, will consist of several levels: 
-1. Learning: about biological background (DNA and sequencing) and how to use the platform. 
+The game, implemented in Galaxy, will consist of several levels:
+1. Learning: about biological background (DNA and sequencing) and how to use the platform.
 2. Hands on: perform the first guided data analysis.
 3. Expert: change and improve their pipeline for data analysis.
 
-Gamer will in the first two levels collect points by answering questions or finding treasures by following hints. In the third level gamer and reseachter will interactively evaluate dataanalysis of otheres and thereby give and get points. We believe that the integration of society into the scientific both will profit. Citizens will get excited for science and they can help to analyze and improve scientific data. 
+Gamer will in the first two levels collect points by answering questions or finding treasures by following hints. In the third level gamer and reseachter will interactively evaluate dataanalysis of otheres and thereby give and get points. We believe that the integration of society into the scientific both will profit. Citizens will get excited for science and they can help to analyze and improve scientific data.
 
 ## Who are we?
 
@@ -118,15 +118,13 @@ In the sequel, we assume you use miniconda.
 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
 
    ```
@@ -138,4 +136,6 @@ In different terminals:
    ```
    $ conda activate dnanalyzer
    $ ./bin/ari-make.sh <path to slide>
-   ```
+   ```
+
+   If any issue happened while running the last command, use `$kill $(lsof -t -i:9876)` before trying again

environment.yml

@@ -3,11 +3,12 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - ruby
+  - ruby=2.6.6
   - nodejs
   - ffmpeg
   - jq
   - sox
   - imagemagick
-
+  - gxx_linux-64
+