About

RNA-3D-Hub-core is the backend for the RNA 3D Hub.

RNA-3D-Hub-core contains:

1. FR3D is included as a submodule.

2. Matlab code for extracting and clustering RNA 3D motifs.

3. Python code responsible for importing non-redundant lists and motif atlas releases into the database, and id assignment to motifs and non-redundant equivalence classes.

Documentation

Detailed documentation on this can be found at readthedocs.

Requirements

• python 2.7 or newer (not tested with Python 3)
• matlab R2007b or newer
• MySQL server
• mlabwap for linking Matlab with Python
• SQLAlchemy for connecting to the database
• fr3d.py
• optional: py.test for running Python unit tests

Installation

1. Download the source code:

   $ git clone https://github.com/AntonPetrov/RNA-3D-Hub-core.git

2. Install Matlab

3. Create a config file, using the template found in: conf/motifatlas.json.txt. By default the pipeline will read the config file in conf/motifatlas.json, but this can be changed.

4. Create the MySQL database(s) specified in the config file.

5. Submodule initialization git submodule init git submodule update

6. Install all dependencies. This can be done by doing pip install -f requirements.txt. This will include nosetests for testing as well.

Testing

The software suite includes test datasets for motifs and non-redundant lists.

Unit tests create a special testing environment and shouldn't interfere with the development or the production versions of the resource. Testing requires that a conf/bootstrap.json config file exists. This will be read for all configuration information. It is strongly recommended that this be a separate database from the production database.

To run unit tests with py.test:

$ py.test

Logging and email notifications

Python logging is configurable. See the section on Configuration for details on how to define the file to log to. By default logging goes to stdout.

Matlab programs add their log messages to a file:

MotifAtlas/logs/rna3dhub_log.txt

The log file is refreshed each time the programs are run.

Some programs email this log file using the information specified in the email section of the config file.

Directory structure

All python code is stored in pymotifs/. The FR3D submodule is stored in FR3D/. The folder FR3D/PDBFiles is used to store all downloaded cif files. In addition, any cached files will be stored there as well. FR3DMotifs contains matlab code needed to process motifs. MotifAtlas is used to store motif atlas specific files.

Usage

The main program that triggers the update is bin/pipeline. To run a full update, do bin/pipeline update --all. This will run all stages of the pipeline on all RNA containing structures. If you want to only run one stage of the pipeline, such as downloading all pdbs, simply do bin/pipeline download --all. For details on what stages are available do bin/pipeline help. If you only want to run the pipeline on one file or more files, simply do: bin/pipeline download 2AW7 1J5E.

When run as a cronjob, you must export a system variable that defines the matlab command string for mlabwrap like so:

export MLABRAW_CMD_STR=/Applications/MATLAB_R2007b/bin/matlab

An example crontab file that runs the update every friday can be found in files/examples/update.cron.

Configuration

This requires that any firewall you are using allow passive FTP connections.