Building all the recipes

Start with a blank Ubuntu 14.04 LTS system.


apt-get update
apt-get -y install screen git curl gcc make g++ python-dev unzip \
        default-jre pkg-config libncurses5-dev r-base-core \
        r-cran-gplots python-matplotlib sysstat samtools python-pip \

pip install virtualenv

As a user, check out:

cd ~/
mkdir dev
cd dev
git clone
git clone
git clone
git clone

python -m virtualenv ipy7 --system-site-packages
. ipy7/bin/activate

cd khmer
git checkout feature/collect_reads
python install

And now grab recipes & build:

pip install sphinx

cd ~/dev/
git clone recipes
cd recipes
make all

Writing recipes - guidelines

Use the recipe in 001 as a guideline.

A few points –

  • make sure that there is a target for the last thing produced by the script, and that this target depends on the ReST file.
  • small output files (figures, etc.) that are necessary to render the ReST files on github should be included in the repository.
  • put ‘set -e’ at the top of your literate resting shell commands so that the script exits with an error message when a command fails. I believe ‘|| 1’ can be used in situations where you want an error to be OK.

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github.
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