Unable to run Roary plots on CLIMB

Ebenn · March 8, 2018, 1:14pm

Good day @mattbull,
I have created a core genome with roary and am now interested in running roary plots, using the command, roary_plots.py name_of_your_newick_tree_file.tre gene_presence_absence.csv. I am following the protocol from Andrew page (http://sanger-pathogens.github.io/Roary/ ) however it appears some of the dependencies needed to run roary plots aren’t installed by default. Please, can you help?
I am not able to install the needed dependencies following the guidelines here,

gist.github.com

https://gist.github.com/mgalardini/6a227baeb955bf97d92d

roary.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Roary pangenome plots\n",
    "============="
   ]
  },

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roary.py

#!/usr/bin/env python
# Copyright (C) <2015> EMBL-European Bioinformatics Institute

# This program is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of

This file has been truncated. show original

Thanks for your kind assistance.
Ebenn

mattbull · March 9, 2018, 9:41am

roary_plots.py and roary.ipynb aren’t dependencies of Roary per se, they were developed by Marco Galardini to provide some additional summary plots at the end of the Roary process, which is why they aren’t included with the standard Roary install on GVL.

The Roary guys do provide the contributed scripts in their repo though, so you can either:

git clone https://github.com/sanger-pathogens/Roary.git
cd Roary/contrib/roary_plots

to find the scripts, or you can download them directly from GitHub:

wget https://raw.githubusercontent.com/sanger-pathogens/Roary/master/contrib/roary_plots/roary_plots.py
wget https://github.com/sanger-pathogens/Roary/blob/master/contrib/roary_plots/roary_plots.ipynb

Ebenn · March 9, 2018, 12:52pm

Hi mattbull,
Many thanks for this!
roary plots is now installed.

Cheers,
Ebenn

system · March 15, 2018, 1:14pm

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