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.
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