CSD3 – Cambridge Service for Data Driven Discovery

CI jsDelivr

This repository details use of many software for generic purpose and genetic analysis; over time they largely become entries of the ceuadmin modules which are ready to use.

jekyll-rtd-theme
csd3
System
...
Acknowledgement
A. Setup
ABCtoolbox
...
Visual Studio Code
B. ensmebl-vep
gwas2vcf
...
Synase
brms
...
xlsx

(Source at Mermaid live editor https://tinyurl.com/k6efyyj8)

graph LR;
jekyll-rtd-theme --> csd3
csd3 --> system[<a href="https://cambridge-ceu.github.io/csd3/systems/" style="font-size: 25px;font-size:90%">THE SYSTEM</a>]
csd3 --> Python[<a href="https://cambridge-ceu.github.io/csd3/Python/" style="font-size: 25px;font-size:90%">Python packages</a>]
csd3 --> R[<a href="https://cambridge-ceu.github.io/csd3/R/" style="font-size: 25px;font-size:90%">R packages</a>]
csd3 --> applications[<a href="https://cambridge-ceu.github.io/csd3/applications/" style="font-size: 25px;font-size:90%">APPLICATIONS</a>]
csd3 --> cardio[<a href="https://cambridge-ceu.github.io/csd3/cardio//" style="font-size: 25px;font-size:90%">APPLICATIONS</a>CARDIO</a>]
system --> System
system --> sysdot["..."]
system --> Acknowledgement
system --> setup["A. Setup"]
applications --> ABCtoolbox
applications --> appdot["..."]
applications --> vsc["Visual Studio Code"]
applications --> vep["B. ensmebl-vep"]
Python --> gwas2vcf
Python --> Pythondot["..."]
Python --> Synase
R --> brms
R --> Rdot["..."]
R --> xlsx

Outside csd3 and under Fedora 43, which furnishes R development, the following is necessary

# install
sudo dnf install parallel ruby ruby-devel rubygems nodejs npm
sudo npm install -g prettier
bundle install
npm install
npm audit fix --force

# test
parallel --version
bundle exec jekyll --version
node --version
npm --version
make build

# ruby 3.2.9
# curl -q -fL -o ruby-3.2.9.tar.gz https://cache.ruby-lang.org/pub/ruby/3.2/ruby-3.2.9.tar.gz
# ./configure "--prefix=$HOME/.rbenv/versions/3.2.9" --enable-shared --with-ext=openssl,psych,+
# make -j 1
sudo dnf install rbenv ruby-build
rbenv install 3.2.9
echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.bashrc
echo 'eval "$(rbenv init - bash)"' >> ~/.bashrc
source ~/.bashrc
rbenv global 3.2.9
rbenv rehash
rm -rf ~/.local/share/gem
rm -rf ~/.bundle
rm -rf vendor/bundle
rm -rf node_modules
rm -f Gemfile.lock package-lock.json
gem install bundler
bundle install
npm install
make build

# ruby 2.7.8
# install build deps
sudo dnf groupinstall "Development Tools"
sudo dnf install \
  gcc gcc-c++ make patch readline readline-devel zlib zlib-devel \
  libyaml-devel libffi-devel openssl-devel gdbm-devel ncurses-devel rust

# install older compatible ruby
rbenv install 2.7.8

# use it for this project
cd ~/cambridge-ceu/csd3
rbenv local 2.7.8

# refresh shims
rbenv rehash

# verify
ruby -v
# should show 2.7.8

# clean broken gems from ruby 3.2 attempts
rm -rf vendor/bundle
rm -rf .bundle
rm -f Gemfile.lock

# install bundler compatible with old jekyll
gem install bundler -v 2.4.22

# install gems
bundle _2.4.22_ install

# install node deps
npm install

# build
make build