Installing Prokka
=================

We're going to use the `Prokka software
<http://www.vicbioinformatics.com/software.prokka.shtml>`__ to
annotate some newly assembled bacterial genomes.

We have to download and install a lot of stuff, though -- estimated ~15
-20 minutes.

First, we need to install BioPerl and NCBI BLAST+; for this we'll use
the Debian Linux package installer, 'apt-get'::

   apt-get update
   apt-get -y install bioperl ncbi-blast+

Now download and unpack Prokka::

   cd /mnt
   curl -O http://www.vicbioinformatics.com/prokka-1.7.tar.gz
   tar xzf prokka-1.7.tar.gz 

Prokka depends on a lot of other software, too; so we'll need to install
all of that.

Install `HMMER <http://hmmer.janelia.org/>`__::

   curl -O ftp://selab.janelia.org/pub/software/hmmer3/3.1b1/hmmer-3.1b1.tar.gz
   tar xzf hmmer-3.1b1.tar.gz 
   cd hmmer-3.1b1/
   ./configure --prefix=/usr && make && make install

Install `Aragorn <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373265/>`__::

   cd /mnt
   curl -O http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.36.tgz
   tar -xvzf aragorn1.2.36.tgz
   cd aragorn1.2.36/
   gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.36.c
   cp aragorn /usr/local/bin

Install `Prodigal <http://prodigal.ornl.gov/>`__::

   cd /mnt
   curl -O http://prodigal.googlecode.com/files/prodigal.v2_60.tar.gz
   tar xzf prodigal.v2_60.tar.gz 
   cd prodigal.v2_60/
   make
   cp prodigal /usr/local/bin


Install `tbl2asn <http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/>`__::

   cd /mnt
   curl -O ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
   gunzip linux64.tbl2asn.gz 
   mv linux64.tbl2asn tbl2asn
   chmod +x tbl2asn
   cp tbl2asn /usr/local/bin

Install `GNU Parallel <http://www.biostars.org/p/63816/>`__::

   cd /mnt
   curl -O http://ftp.gnu.org/gnu/parallel/parallel-20130822.tar.bz2
   tar xjvf parallel-20130822.tar.bz2
   cd parallel-20130822/
   ls
   ./configure && make && make install

Install `Infernal <http://infernal.janelia.org/>`__::

   cd /mnt
   curl -O http://selab.janelia.org/software/infernal/infernal-1.1rc4.tar.gz
   tar xzf infernal-1.1rc4.tar.gz 
   cd infernal-1.1rc4/
   ls
   ./configure && make && make install

To run prokka on a set of assembled contigs, type
``/mnt/prokka-1.7/bin/prokka genomefile --outdir annot --prefix
annot``, replacing ``genomefile`` with the name of the file containing
the contigs.  The results will be placed in the directory ``annot``;
the protein coding genes will be in ``annot/annot.faa``, which you can
run ``head`` on.