Differences

This shows you the differences between two versions of the page.

--- metaphlan2-software [2019/12/22 08:16] – aorth
+++ metaphlan2-software [2021/08/29 09:12] (current) – removed aorth
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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
-  * 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.