Installation

Code installation

To install the benchmarking suite from the repository, clone the latest version from github:

git clone https://github.com/cgat-developers/cgat-daisy
cd cgat-daisy
python setup.py install

Alternatively, daisy release packages are available via pypi:

pip install cgat-daisy

and conda:

conda install -c bioconda cgat-daisy

Configuration

Daisy connects to the cluster. To set global configuration values, it looks for the file daisy.yml in the user’s home directory. If it exists it will be used to set default values. A typical configuration file might look like this:

cluster:
  queue: all.q
  options: ""
  priority: -10
  memory_resource: h_vmem
  memory_default: 4G
  parallel_environment: shmem

For more information, see Parameterisation.

External dependencies

System packages

Daisy requires certain system packages installed. Below is an (incomplete) list:

  • libsqlite3-dev
  • libfreetype6
  • libfreetype6-dev
  • libpq-dev
  • gcc
  • libjpeg-dev
  • libx11-dev

Using the Cluster

In order to use the cluster, libdrmaa.so needs to be installed and in LD_LIBRARY_PATH. For SGE, the environment variable SGE_ROOT needs to set, for example:

export SGE_ROOT=/var/lib/gridengine

Tools and Metrics

The Task Library within the repository contains Runners to execute tools and metrics, but these are only wrappers. The actual tools and metrics need to be installed separately.

By default, tools and metrics are assumed to be in your PATH and accessible from both the submit and execution hosts. The system also assumes that files on the submit and execution hosts are accessible from the same paths.

Database setup

Daisy can work with several database engines. For sqlite, no additional setup is required. For postgresql, Daisy needs to connect to an existing database. The database needs to be set up prior to running a daisy and appropriate user permissions need to have been set up.

With postgresql it is possible to use schema to organise metric tables. Schemas also need to be created beforehand, they will not be created by Daisy.