Difference between revisions of "MetaPhlAn2"
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(Created page with "Category:SoftwareCategory:BiologyCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|metaphlan2}} |{{#vardefine:url|https://bitbucket.org/bio...") |
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DOC - documentation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_UTI - utils directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_EXE - example directory |
| + | * METAPHLAN_BOWTIE2_DB - reference database directory | ||
<!--Configuration--> | <!--Configuration--> | ||
| Line 35: | Line 36: | ||
|}} | |}} | ||
<!--Run--> | <!--Run--> | ||
| − | {{#if: {{#var: exe}}|==Additional Information== | + | {{#if: {{#var: exe}}1|==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: | |
| + | |||
| + | <code>--index mpa_v30_CHOCOPhlAn_201901 --bowtie2db $METAPHLAN_BOWTIE2_DB</code> | ||
|}} | |}} | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
{{#if: {{#var: job}}|==Job Script Examples== | {{#if: {{#var: job}}|==Job Script Examples== | ||
| − | + | ||
|}} | |}} | ||
<!--Policy--> | <!--Policy--> | ||
Latest revision as of 19:28, 2 June 2022
Description
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