Pre-requisites
Hydra requires Java 1.6+. All other tools are wrapped in a Conda environment, see below.
1. Get Conda
conda is available as part of the miniconda package <http://conda.pydata.org/miniconda.html>_.
.. note::
If you're using a module system such as on the shared computing cluster (SCC) at Boston University you can just load a preinstalled version:
.. code:: bash
module purge
module load anaconda2/4.3.02. Set Environment and Build Paths::
export CONDA_ENVS_PATH=<WORKING_DIR>/conda-envs
export CONDA_BLD_PATH=<WORKING_DIR>/conda-bld3. Create Dev Environment
Use conda to install a basic developement environment::
conda env create \ montilab/dev_env \ -p ./dev_env
This will create a `./dev_env folder that stores all the files needed to run the pipeline. For more details, please refer to the Developer's Guide. (LINK)
4. Install all necessary R packages Activate the environment so you have access to the R version that the pipeline uses::
source activate ./dev_env
Start R::
R
Within R install all necessary packages::
require(devtools)
install_git("http://github.com/nachocab/clickme.git")Activate the environment (follow the instructions provided by conda following the environment's creation)::
source activate ./dev_env
Then you can run the pipeline, while providing your parameter file.
Example::
hydra-rnaseq -p param.txt
A detailed description of the parameter file is provided here <docs/user_docs/parameters.rst>__ and an example is located here here <parameters_example.txt>__ .
A detailed user documentation is provided here <docs/user_docs/index.rst>__. For advanced users that are contributing to the development such as adding additional modules a documentation is provided here <docs/dev_docs/index.rst>__