MetaPhlAn2 is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
module spider metaphlan2 to find out what environment modules are available for this application.
- HPC_METAPHLAN2_DIR - installation directory
- HPC_METAPHLAN2_BIN - executable directory
- HPC_METAPHLAN2_DOC - documentation directory
- HPC_METAPHLAN2_UTI - utils directory
- HPC_METAPHLAN2_EXE - example directory
- METAPHLAN_BOWTIE2_DB - reference database directory
There have been cases where metaphlan tries to download the latest database before running. The latest database (mpa_v30_CHOCOPhlAn_201901) is available at $METAPHLAN_BOWTIE2_DB, therefore, to skip the database update step, the following needs to be specified in the script:
--index mpa_v30_CHOCOPhlAn_201901 --bowtie2db $METAPHLAN_BOWTIE2_DB