MetaPhlAn's use of PhyloPhlAn in a read-only software stack

Microbial community profiling MetaPhlAn
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Summary question: How can i prevent MetaPhlAn from using the default python library location as PhyloPhlAn’s config directory when that location might need to be read-only?

I’m a HPC admin who has been tasked with troubleshooting a MetaPhlAn setup. The way we distribute software necessarily makes the software’s path non-writable, for a variety of network load and security based reasons.

How can I configure these guys to talk nicely together and use a dir under the user’s home automatically? I have seen that PhyloPhlAn’s code should support redirection of this output, but I haven’t been able to find how to do this with MetaPhlAn.

If this isn’t currently possible I understand, but many HPC sites will have this issue.

Of course, I understand that a standard method of getting around this is to install the software into a conda environment in the home of every user who wants to use it. That’s what i’ll fall back to if it isn’t possible to get around this issue.

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The phylophlan_write_default_configs.sh script generates the configuration files in a given directory outd passed by parameter.
StrainPhlAn has the phylophlan_configuration parameter in which a non-default location of the PhyloPhlAn configuration files can be passed, so each users could create the configuration files in their writable home folders and then, when using StrainPhlAn, always use the aforementioned parameter.

Obviously, if someone is interested in only running MetaPhlAn, this is can avoided since MetaPhlAn does not use PhyloPhlAn

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Ah, I see. The user is actually using StrainPhlAn and didn’t initially differentiate. There’s no problem here.

Thanks for your time.