metaphlan2-software
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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
Usage
See which versions of metaphlan2 are available:
$ module avail metaphlan2
Load one version into your environment and run it:
$ module load metaphlan2/2.9.5 $ metaphlan2
Note: Please specify the number of CPU (processors) to use when you run metaphlan2. For example:
$ metaphlan2.py SRS014459-Stool.fasta.gz --input_type fasta --nproc 4 > SRS014459-Stool_profile.txt
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:
$ 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
Note: check the mpa_latest
file on metaphlan2's downloads page to see which is the latest database during installation.
metaphlan2-software.1577002586.txt.gz · Last modified: 2019/12/22 08:16 by aorth