Installation

We recommend to install the R-package via devtools:

library(devtools)
install_github(repo = "loosolab/PARrOT/PARrOT",host = "github.molgen.mpg.de/api/v3")

The analysis can also be performed with the help of the docker container, which can be pulled from here.

Also we recommend Python 2.7.13 and Debian or Ubuntu as operating system. For this the install of the graph-tool library can be executed by:

For Debian, add the following lines to your /etc/apt/sources.list,

deb http://downloads.skewed.de/apt/DISTRIBUTION DISTRIBUTION main
deb-src http://downloads.skewed.de/apt/DISTRIBUTION DISTRIBUTION main

where DISTRIBUTION can be any one of

stretch, buster, sid

For Ubuntu, add the following lines

deb http://downloads.skewed.de/apt/DISTRIBUTION DISTRIBUTION universe
deb-src http://downloads.skewed.de/apt/DISTRIBUTION DISTRIBUTION universe

where DISTRIBUTION can be any one of

xenial, yakkety, zesty, artful, bionic, cosmic

After running apt-get update, the package can be installed with

apt-get install python-graph-tool

If you want to verify the packages, you should use the public key 612DEFB798507F25, which can be done with the command: apt-key adv --keyserver pgp.skewed.de --recv-key 612DEFB798507F25 Afterwards, you can run apt-key list, which should give you the following details about the key:

pub   rsa4096 2013-10-17 [SC] [expires: 2020-10-23]
      793C EFE1 4DBC 851A 2BFB  1222 612D EFB7 9850 7F25
uid           [ unknown] Tiago de Paula Peixoto <tiago@skewed.de>
uid           [ unknown] Tiago de Paula Peixoto <t.peixoto@bath.ac.uk>
uid           [ unknown] Tiago de Paula Peixoto <tiago@itp.uni-bremen.de>
sub   rsa4096 2013-10-17 [S] [expires: 2020-10-23]
sub   rsa4096 2013-10-17 [E] [expires: 2020-10-23]
sub   rsa4096 2017-10-24 [S] [expires: 2020-10-23]
sub   rsa4096 2017-10-24 [E] [expires: 2020-10-23]
sub   rsa4096 2017-10-24 [A] [expires: 2020-10-23]

Installation instructions for other OS can be obtained here