Installation

The following sections describe how to install the cgatshowcase framework. Since there are very minimal dependancies the installation of the code should not take too long. The main dependancies are cgat-core, cgat-apps, kallisto, deseq2, biomart, tximport and genomeinfodb.

Installation using conda

The most convinient way to use our code is to install the software using conda. First you will need to install conda using miniconda or anaconda and following the instructions here. (we recomend miniconda rather than anaconda)

Once you have conda installed then to install cgat-showcase please do the following:

conda install -c cgat cgatshowcase

This should install all of the dependancies and you should be read to proceded to the Writing workflows and Tutorial section. However, conda is currently having issues with speed of installation. This is related to the solver and is something that is known and the conda developers are workin on new fixes for this. Please see conda issue for more information.

Pip installation

Alternatively, cgatshowcase can also be installed using pypi:

pip install cgatshowcase

However, the dependancies will have to be installed seperately.

Manual installation

To obtain the latest code, check it out from the public git repository and activate it:

git clone https://github.com/cgat-developers/cgat-core.git
cd cgat-core
python setup.py develop

Once checked-out, you can get the latest changes via pulling:

git pull

Installing additonal software

When building your own workflows we recomend using conda to install software into your environment where possible.

This can easily be performed by:

conda search <package>
conda install <package>