====== metaphlan2 ======

MetaPhlAn2 is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.

===== Information =====

  * Version: 2.9.5
  * Added: December, 2019
  * Link: https://bitbucket.org/biobakery/biobakery/wiki/metaphlan2

===== Usage =====

See which versions of metaphlan2 are available:
<code>$ module avail metaphlan2</code>

Load one version into your environment and run it:
<code>$ module load metaphlan2/2.9.5
$ metaphlan2</code>

**Note:** Please specify the number of CPU (processors) to use when you run metaphlan2. For example:

<code>$ metaphlan2.py SRS014459-Stool.fasta.gz --input_type fasta --nproc 4 > SRS014459-Stool_profile.txt</code>

The number of CPUs requested with the ''--nproc'' option should be the same as the number requested in your SBATCH, ie ''#SBATCH -n 4''.

===== Installation ======

Notes from the sysadmin during installation:

<code>$ cd /tmp
$ hg clone https://bitbucket.org/biobakery/metaphlan2
$ cd metaphlan2
$ hg tags
$ hg checkout 2.9.5
$ sudo mkdir -p /export/apps/metaphlan2/2.9.5
$ sudo chown aorth /export/apps/metaphlan2/2.9.5
$ python3 -m venv /export/apps/metaphlan2/2.9.5
$ source /export/apps/metaphlan2/2.9.5/bin/activate
$ pip3 install -U pip setuptools
$ pip3 install -U numpy scipy pandas biopython matplotlib
$ sudo cp -r . /export/apps/metaphlan2/2.9.5
$ sudo mkdir /export/apps/metaphlan2/2.9.5/metaphlan_databases
$ wget https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_v295_CHOCOPhlAn_201901.tar
$ sudo mv mpa_v295_CHOCOPhlAn_201901.tar /export/apps/metaphlan2/2.9.5/metaphlan_databases</code>

**Note:** check the ''mpa_latest'' file on [[https://bitbucket.org/biobakery/metaphlan2/downloads/|metaphlan2's downloads page]] to see which is the latest database during installation.