Prokka installation

If you did not install Prokka (annotation tool), BacPipe will produce: Please select a valid prokka path or switch it off

Solution:

Installation

Before the main install can begin you need to install some system packages:

Centos/Fedora/RHEL (RPM)

sudo yum install perl-Time-Piece perl-XML-Simple perl-Digest-MD5 git java perl-CPAN perl-Module-Build
sudo cpan -i Bio::Perl  # if you don't have Bioperl installed (it will be tedious)

Ubuntu/Debian/Mint (APT)

sudo apt-get install libdatetime-perl libxml-simple-perl libdigest-md5-perl git default-jre bioperl

Mac OS X

sudo cpan Time::Piece XML::Simple Digest::MD5 Bio::Perl

There are currently 3 ways to install the main Prokka software:

Github, Tarball or Homebrew.

Github

Choose somewhere to put it, for example in your home directory (no root access required):

% cd $HOME

Clone the latest version of the repository:

% sudo apt install git (if you don't have git installed)
% git clone https://github.com/tseemann/prokka.git
% ls prokka

Index the sequence databases

% prokka/bin/prokka --setupdb

Homebrew

Homebrew is a package manager which allows users to easily install complex software in their home directory. Instructions for installing it are available for Linux and Mac OS X.

Ensure you have brew installed:

% brew

Make sure you have the homebrew-science tap/channel enabled:

% brew tap homebrew/science
% brew update

Install Prokka and all its dependencies:

% brew install prokka --HEAD

Tarball

WARNING: this method gives you very old version of prokka. The brew or github methods are preferred!

Download the latest prokka-1.xx.tar.gz archive from http://www.bioinformatics.net.au/software.prokka.shtml

% wget http://www.vicbioinformatics.com/prokka-1.11.tar.gz

Choose somewhere to put it, for example in your home directory (no root access required):

% cd $HOME
% tar zxvf prokka-1.11.tar.gz
% ls prokka-1.11

Dependencies

Mandatory

BioPerl
Used for input/output of various file formats (http://bioperl.org/) Stajich et al, The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002 Oct;12(10):1611-8.

we have already installed it for BacPipe
GNU Parallel
A shell tool for executing jobs in parallel using one or more computers (http://www.gnu.org/software/parallel/_ O. Tange, GNU Parallel - The Command-Line Power Tool, ;login: The USENIX Magazine, Feb 2011:42-47.
BLAST+
Used for similarity searching against protein sequence libraries
Camacho C et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009 Dec 15;10:421.
Prodigal
Finds protein-coding features (CDS) (https://code.google.com/p/prodigal/) Hyatt D et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010 Mar 8;11:119.
TBL2ASN Prepare sequence records for Genbank submission (ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/) Tbl2asn home page

wholeGenomeSequencingAnalysisPipeline / BacPipe