Permanently set custom database path?

Microbial community profiling MetaPhlAn
#1

Is there a metaphlan setting analagous to humann_config that allows me to set the default database for metaphlan to use? The default conda install on my cluster points to the home directory, which is on a slow-ish drive. I know I can use --bowtie2db /path/to/db, but is there a way to to this permanently?

The help output implies that setting $METAPHLAN_BOWTIE2_DB might work, but it’s not set by default.

1 Like
#2

Hi Kevin, unfortunately no, now the default is set as the MetaPhlAn installation folder. METAPHLAN_BOWTIE2_DB is set as metavar, a help string for the --bowtie2db parameter, but it’s feasible include the possibility to set the default value of the parameter as the content of METAPHLAN_BOWTIE2_DB, if the env variable is set.

#3

I think this would be nice, but not critical. I’ll just add the flag to my workflow. Thanks!