Python modules

There are several extra python module requirements that are needed and are summarized in the following table.

These modules might have extra dependencies. Details of the list of all modules required are listed in BacterialTyper/config/python/python_requirements.txt. And accessible here:

Although these dependencies will be fulfilled during the BacterialTyper installation with pip, you might be interested in installing them yourself.

Using pip we can install them all at a glance.

pip install -r ./BacterialTyper/config/python/python_requirements.txt

But again, following installation recommendations, we encourage you to create and install them within a virtual environment (See section: Python environment section for details).

You can test the presence of these python modules using the BacterialTyper config module. Once you identified the missing dependencies and minimum versions required you can either install them and set them available within your PYTHONPATH or environment or you can execute the BacterialTyper config with install option.

Perl packages

Although we tried to focus on Python as the main programming language for BacterialTyper there are some scripts that are in perl. This is due to simplicity as this functions were previously written in other projects and we just re-used the code. As time goes by, we would like to reduce the perl code to a minimum and rewrite it in python.

The perl packages required within these scripts are core modules of perl and should be available within your installation. These modules are listed in file BacterialTyper/config/perl/perl_dependencies.csv, which is shown below:

module_name

module

type_module

version

strict

strict

core

1.09

warnings

warnings

core

1.32

Cwd

Cwd

core

3.62

Data_dumper

Data::Dumper

core

2.170

File-Copy

File::Copy

core

2.30

File-Basename

File::Basename

core

2.85

File-Spec

File::Spec

core

3.62

File-Path

File::Path

core

2.12

File-Temp

File::Temp

core

0.2304

FindBin

FindBin

core

1.51

List-Util

List::Util

core

1.5

Getopt-long

Getopt::Long

core

2.5

You can test the presence of these perl modules using the BacterialTyper config module.

Software dependencies

Also, several software packages are also required. They are listed in BacterialTyper/config/software/dependencies.csv, which is shown below:

soft

version_cmd

get_version

min_version

soft_name

fastqc

-v

FastQC.*v([0-9.]+).*

0.11.4

fastqc

dimob

‘’

Version: v([0-9.]+).

2019.06.27

Dimob.pl

kma

-v

KMA-([0-9.]+).*

1.2.2

kma

iqtree

–version

([0-9.]+)

2.0.5

iqtree2

prokka

-v

prokkas([0-9.]+).*

1.12

prokka

spades

–version

SPAdes.*s+v([0-9.]+).*

3.15.2

spades.py

trimmomatic

-version

([0-9.]+).*

0.36

trimmomatic

snippy

–version

snippy ([0-9.]+).*

3

snippy

efetch

-help

efetch ([0-9.]+)

13.6

efetch

esearch

-help

esearch ([0-9.]+)

13.6

esearch

xtract

-version

([0-9.]+)

13.6

xtract

blastn

-version

blastn:s([0-9.]+)

2.5

blastn

makeblastdb

-version

makeblastdb:s([0-9.]+)

2.5

makeblastdb

tblastn

-version

tblastn:s([0-9.]+).*

2.5

tblastn

Rscript

–version

.*versions([0-9.]+).*

3.5.1

Rscript

java

-version

versions"([0-9..*_.*]+)"

1.8.0_172

java

python

–version

([0-9.]+)

3.6

python

perl

–version

v([0-9].[0-9]+.[0-9])

5.18.1

perl

make

–version

GNU Make ([0-9].[0-9].*)

4

make

git

–version

git version ([0-9].[0-9]+.[0-9])

2.1.0

git

augustus

–version

AUGUSTUS.*(([0-9.]+)).*

3.2.1

augustus

bowtie2

–version

.*bowtie2.*version (.*)$

2.1.0

bowtie2

busco

–version

BUSCOs([0-9.]+)

5.1.2

busco

generate_plot

-h

(usage.*)

1

generate_plot.py

cdhit

‘’

CD-HIT version ([0-9.]+) (

4.6

cd-hit-est

hmmsearch

-h

HMMERs([0-9]..*)s

3.1b2

hmmsearch

nucmer

–version

([0-9]+.[0-9.]+.*$)

3.1

nucmer

agrvate

–version

agrvatesv([0-9]..*)

1.0

agrvate

staphopia-sccmec

–version

staphopia-sccmecs([0-9]..*)

1.0.0

staphopia-sccmec

amrfinder

–version

([0-9]..*)

3.11.26

amrfinder

amrfinder_update

–version

([0-9]..*)

3.11.26

amrfinder_update

kraken2

–version

([0-9]..*)

2.1.3

kraken2

bracken

-v

v([0-9]..*)

2.9

bracken

mlst

–version

mlst ([0-9]..*)

2.23.0

mlst

Most of the software are common software that any person doing bioinformatics should have, so you might have already available within your system.

You might need to have installed some basic libraries:

  • default java run time environment (jre),

  • C-compiler

  • zlib development files

  • perl libraries

  • Bio::Perl

## Ubuntu/Debian/Mint
sudo apt install -y git
sudo apt install -y libz-dev
sudo apt install -y build-essential
sudo apt install -y cmake
sudo apt install -y python3 python3-dev python-dev python3-venv python-pip
sudo apt install -y libssl-dev libffi-dev libxml2-dev libxslt1-dev zlib1g-dev
sudo apt install -y default-jre
sudo apt install -y libdatetime-perl libxml-simple-perl 
sudo apt install -y bioperl
sudo cpan Bio::Perl

You can test for any missing software dependencies using the BacterialTyper config module. Once you identified the missing dependencies and minimum versions required you can either install them and set them available within your $PATH or you can execute the BacterialTyper config with install option.

Third party software

Additionally, within the BacterialTyper MGE module there is an optional analysis that determines the pathogenic islands within the genome. The tool that we employ for this purpose is named IslandPath-DIMOB (IslandPath [1]) and we distribute it along BacterialTyper. See additional details in the API section for Third-party Software.

This third party software requires multiple perl modules and in turn, depend on many others, making the installation and distribution quite difficult. As we established this analysis as supplementary, so far, we would not take care of fulfilling the multiple requirements of this tool. This packages are listed in here:

Package

Version

Type_module

Carp

1.50

core

POSIX

1.84

core

Config-Simple

4.58

install

ExtUtils-Config

0.008

install

ExtUtils-Helpers

0.026

install

ExtUtils-InstallPaths

0.012

install

Module-Build-Tiny

0.039

install

MooseX-Singleton

0.30

install

BioPerl

1.7.7

install

We encorage to install these modules using CPAN (https://www.cpan.org/) or any other perl package installer of your interest.

To test the presence of these additional perl modules, you can also use the BacterialTyper config module.