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metaphlan-software [2021/08/29 08:06] – created aorthmetaphlan-software [2023/07/19 08:36] (current) – aorth
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 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling. MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
  
-  * Latest Version: 3.0.13+  * Latest Version: 4.0.6
   * Added: August, 2021   * Added: August, 2021
 +  * Updated: July, 2023
   * Link: https://github.com/biobakery/MetaPhlAn   * Link: https://github.com/biobakery/MetaPhlAn
  
 ===== Usage ===== ===== Usage =====
-Show all available versions of metaphlan:+Show all available versions:
 <code>$ module avail metaphlan</code> <code>$ module avail metaphlan</code>
  
 Load one version into your environment and run it: Load one version into your environment and run it:
  
-<code>$ module load metaphlan/3.0.13+<code>$ module load metaphlan/4.0.6
 $ metaphlan -h</code> $ metaphlan -h</code>
  
 **Note:** Please specify the number of CPU (processors) to use when you run metaphlan. For example: **Note:** Please specify the number of CPU (processors) to use when you run metaphlan. For example:
  
-<code>metaphlan metagenome.fastq --input_type fastq --nproc 4 -o /var/scratch/profiled_metagenome.txt</code>+<code>$ metaphlan metagenome.fastq --input_type fastq --nproc 4 -o /var/scratch/profiled_metagenome.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''. The number of CPUs requested with the ''--nproc'' option should be the same as the number requested in your SBATCH, ie ''#SBATCH -n 4''.
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 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
  
-<code>$ sudo mkdir -p /export/apps/metaphlan/3.0.13 +<code>$ module load python/3.9 
-$ sudo chown aorth:aorth /export/apps/metaphlan/3.0.13 +$ sudo mkdir -p /export/apps/metaphlan/4.0.6 
-$ module load python/3.8 +$ sudo chown aorth:aorth /export/apps/metaphlan/4.0.6 
-$ python3 -m venv /export/apps/metaphlan/3.0.13 +$ mkdir /export/apps/metaphlan/4.0.6/.venv 
-$ source /export/apps/metaphlan/3.0.13/bin/activate +$ python -m venv /export/apps/metaphlan/4.0.6/.venv 
-$ pip install --upgrade setuptools pip +$ source /export/apps/metaphlan/4.0.6/.venv/bin/activate 
-$ pip install metaphlan==3.0.13+$ pip install --upgrade pip setuptools wheel 
 +$ pip install metaphlan==4.0.6 
 +$ module load bowtie2/2.5.0
 $ metaphlan --install $ metaphlan --install
-$ sudo chown -R root:root /export/apps/metaphlan/3.0.13</code>+$ sudo chown -R root:root /export/apps/metaphlan/4.0.6</code>
metaphlan-software.1630224388.txt.gz · Last modified: 2021/08/29 08:06 by aorth