If you do not have write permissions to ‘/usr/lib/’, then add the option “–user” to the HUMAnN 2.0 install command.To overwite existing installs of Bowtie2 and Diamond, add the option “–install-option=’–replace-dependencies-install'” to the install command. ![]() To build Diamond from source during the install, add the option “–install-option=’–build-diamond'” to the install command.To bypass the install of Bowtie2 and Diamond, add the option “–install-option=’–bypass-dependencies-install'” to the install command.This command will automatically install MinPath (and a new version of glpk) along with Bowtie2 and Diamond (if they are not already installed).Bowtie2, Diamond, and Minpath will be automatically installed when you install HUMAnN 2.0 You can then add the MetaPhlAn2 folder to your $PATH or you can provide its location when running HUMAnN 2.0 with the option “–metaphlan $DIR” (replacing $DIR with the full path to the MetaPhlAn2 folder). ![]() ![]() When installing HUMAnN 2.0, please also download and install MetaPhlAn 2.0.
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