Coding Workshop

Requirements for Participating in this Workshop

• Code Ocean v2.0 or newer
• Code Ocean API Access Token
  • There are instructions below on how to create one
• Python >=3.8

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Creating an API Access Token

1. Click on the Account icon in the lower lefthand corner.
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2. Click on Access Tokens
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3. Click on Generate new token
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4. Add a name for your new token and select all 4 checkboxes
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5. Click on the Add Token button.
6. Click on Copy to copy the token to your clipboard
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7. Paste the token into your favorite password manager so that it will be available later when we update a configuration file.

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Setting up this capsule in Code Ocean

1. Create a new capsule and select copy from public git

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2. Enter the url for this github repo

   • https://github.com/codeocean/coding_workshop.git

3. Select a starter environment that has python available. The Python (3.8.5, miniconda 4.9.2, jupyterlab 3.0.9) starter environment that came preinstalled with Code Ocean will work.

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4. Click on Edit Post-Install Script

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5. Add the following code to the postinstall script

apt-get update
apt-get install build-essential ca-certificates default-jre libz-dev pigz vim wget -y

conda update conda -y && conda update --all -y
conda install -c conda-forge mamba -y
mamba install -c bioconda fastqc -y

# Code Ocean Aux Tools
pip install -i https://test.pypi.org/simple/ Code-Ocean-Aux-Tools
pip install multiqc

# fastp
mkdir -p /opt && cd /opt
wget http://opengene.org/fastp/fastp
chmod a+x ${PWD}/fastp
ln -s ${PWD}/fastp /usr/local/bin

# Simulated reads generator
mkdir -p /opt && cd /opt
git clone https://github.com/lh3/wgsim.git
cd wgsim
gcc -g -O2 -Wall -o wgsim wgsim.c -lz -lm
ln -s ${PWD}/wgsim /usr/local/bin

6. Add the API token in the config.py file (in the code folder) on the line that has co_api_key = ""

   • The token should be inside the double quotes.

7. Copy your current Code Ocean host name. This will be everything after https:// and before /capsule/ in the URL of your web browser where you access Code Ocean.

   • e.g. https://mybiotechcompany.com/capsule/
   • You would copy mybiotechcompany.com

8. Paste the host name in the config.py file on the line that has co_domain = ""

   • The host name should be inside the double quotes.

9. Add your first name in the config.py file on the line that has user = ""

   • Your first name should be inside the double quotes.

10. You are now ready to participate in the Coding Workshop

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