Difference between revisions of "MetaPhlAn2"

Latest revision as of 19:28, 2 June 2022

Description

metaphlan2 website

MetaPhlAn2 is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.

Environment Modules

Run module spider metaphlan2 to find out what environment modules are available for this application.

System Variables

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

Additional Information

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

@@ Line 29: / Line 29: @@
 * HPC_{{uc:{{#var:app}}}}_UTI - utils directory
 * HPC_{{uc:{{#var:app}}}}_EXE - example directory
+* METAPHLAN_BOWTIE2_DB - reference database directory
 <!--Configuration-->
@@ Line 35: / Line 36: @@
 |}}
 <!--Run-->
-{{#if: {{#var: exe}}|==Additional Information==
+{{#if: {{#var: exe}}1|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+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:
+<code>--index mpa_v30_CHOCOPhlAn_201901 --bowtie2db $METAPHLAN_BOWTIE2_DB</code>
 |}}
 <!--Job Scripts-->
 {{#if: {{#var: job}}|==Job Script Examples==
-See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
 |}}
 <!--Policy-->