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Manuscript builds using Ubuntu 20.04 LTS

This has been tested using Ubuntu 20.04 LTS beta in Virtualbox 6.1 running on macOS 10.13.6 High Sierra. Ubuntu 20.04 LTS is in beta release only at time of writing so be sure to update regularly.

All commands are typed into command line after $ in Ubuntu Terminal app.

1. Ensure Ubuntu is updated

sudo add-apt-repository universe
sudo add-apt-repository multiverse
sudo apt update
sudo apt upgrade

2. Install dependencies

sudo apt install scons
sudo apt install git
sudo apt install bioperl
sudo apt install paml
sudo apt install scipy

sudo apt --yes install \
    libbio-eutilities-perl \
    libbio-tools-phylo-paml-perl \
    libbio-tools-run-alignment-tcoffee-perl

sudo apt --yes install \
    texlive \
    texlive-latex-extra \
    texlive-fonts-extra \
    texlive-font-utils \
    texlive-science \
    texlive-publishers \
    texlive-lang-greek

sudo apt --yes install \
    libmoose-perl \
    libmoosex-strictconstructor-perl \
    libmodule-scandeps-perl \
    libtest-output-perl \
    libstatistics-basic-perl \
    libtext-csv-perl \
    libfile-which-perl

sudo apt install python3-pip

sudo pip3 install weblogo

3. Clone histone-catalogue

git clone https://github.com/af-lab/histone-catalogue.git

4. Build manuscript

cd histone-catalogue
git pull
scons \
    --api_key='xxxxxxxxxxxxxxxxxxx' \
    --email='[email protected]' \
    update manuscript

Print or copy the manuscript.pdf file generated in the histone-catalogue directory.

Notes

  • To refresh all RefSeq data use scons [email protected] update manuscript
    • Executing scons without manuscript will generate figures only as catalogue.pdf
  • Email address is required but is simply recorded in the log file in case NCBI wish to discuss data transfers.
  • API key can be obtained via your MyNCBI page. This is now required for appropraite data transfers.
  • First or refreshed builds take a while to download fresh data from NCBI so it is often convenient to start them in a virtual screen session using screen -DR build