the requirements you mentioned here is related to MetaPhlAn2, which had to use a specific version of
samtools since StrainPhlAn was requiring a specific output format that was kept only to such versions.
If you are not interested in using StrainPhlAn, you can upgrade samtools to a more recent version. The usage of samtools is limited to StrainPhlAn, since MetaPhlAn2 does not uses it internally.
In the latest MetaPhlAn 3.0 recipe, you can use the latest version of
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