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.