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