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MetaPhlAn: Difference between revisions
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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 StrainPhlAn, it is possible to perform accurate strain-level microbial profiling", according to its [https://github.com/biobakery/MetaPhlAn GitHub repository]. While the software stack on our clusters does contain modules for a couple of older versions (2.2.0 and 2.8) of this software, we now expect users to install more recent versions using a [[Python#Creating_and_using_a_virtual_environment | Python virtual environment]]. Wheels are available in our wheelhouse for these more recent versions of the MetaPhlAn software: 3.0.0a1, 3.0.7 and 4.0.2. You should begin by loading certain modules needed by the Python wheel, | 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 StrainPhlAn, it is possible to perform accurate strain-level microbial profiling", according to its [https://github.com/biobakery/MetaPhlAn GitHub repository]. While the software stack on our clusters does contain modules for a couple of older versions (2.2.0 and 2.8) of this software, we now expect users to install more recent versions using a [[Python#Creating_and_using_a_virtual_environment | Python virtual environment]]. Wheels are available in our wheelhouse for these more recent versions of the MetaPhlAn software: 3.0.0a1, 3.0.7 and 4.0.2. You should begin by loading certain modules needed by the Python wheel, | ||
{{Command|module load gcc blast samtools bedtools bowtie2 | {{Command|module load gcc blast samtools bedtools bowtie2 python/3.9}} | ||
after which you can create the virtual environment | after which you can create the virtual environment | ||
{{Command|virtualenv --no-download --clear $HOME/ENV | {{Command|virtualenv --no-download --clear $HOME/ENV}} | ||
You should then enter the virtual environment, | You should then enter the virtual environment, | ||
{{Command|source $HOME/ENV/bin/activate}} | {{Command|source $HOME/ENV/bin/activate}} | ||