Building all the recipes¶

Start with a blank Ubuntu 14.04 LTS system.

Install:

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 \
        ipython-notebook

pip install virtualenv

As a user, check out:

cd ~/
mkdir dev
cd dev
git clone https://github.com/ged-lab/khmer.git
git clone https://github.com/ged-lab/nullgraph.git
git clone https://github.com/ged-lab/khmer-recipes.git
git clone https://github.com/ged-lab/literate-resting.git

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

cd khmer
git checkout feature/collect_reads
python setup.py install

And now grab recipes & build:

pip install sphinx

cd ~/dev/
git clone https://github.com/ged-lab/khmer-recipes.git 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.