mg-process-files

Scripts for processing text files ready for indexing for the RESTful servers as pipelines within the MuG VRE.

Full documentation can be found on ReadTheDocs

Requirements

• bedToBigBed - http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
• HDF5
• Python 2.7.10+
• Python Modules:
  • numpy
  • h5py

Installation

Cloneing from GitHub:

git clone https://github.com/Multiscale-Genomics/mg-process-files.git

To get this to be picked up by pip if part of a webserver then:

pip install --editable .

This should install the required packages listed in the setup.py script.

Installation via pip:

pip install git+https://github.com/Multiscale-Genomics/mg-process-files.git

Configuration file

Requires a file with the name dmp.cnf with the following parameters to define the MongoDB server:

[dmp]
host = localhost
port = 27017
user =
pass =
db = dmp
ftp_root = ftp://ftp.<url_root>