A problem with usearch version

[Ilnam Kang]

Hi,

Are there any method that can make PhyloPhlAn recognize and use usearch version 5.2.32 not located in the system path?

I have another program that is dependent on the usearch version higher than 5.2.32. To be able to use that program conveniently, I have to locate the more recent version of usearch in the system path, which makes PhyloPhlAn not working.

Are there any solution for this problem?

Thanks.

[Francesco Asnicar]

Hi,

Unfortunately, PhyloPhlAn expects to find the "usearch" command in the system path and to be the 5.2.32 version.

A solution could be to write a small bash script that will export the specific usearch version only when running the script, so you don't have to set usearch 5.2.32 always, solving your other dependency problem.

I attached a template of the bash script, you have to set the correct path to where you have usearch 5.2.32 in your system, make sure the command is "usearch", and make also sure that the "python" command in your system is executing Python2, otherwise change it to a python command that runs Python2.

Please, let me know if this solves your problem.

Many thanks,

Francesco

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[Ilnam Kang]

Your script works nicely!!

Thank you very much for your help.

Ilnam

2018년 1월 4일 목요일 오후 6시 40분 57초 UTC+9, francescoasnicar 님의 말: