SegataLab / panphlan

PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
MIT License
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panphlan bioconda recipe is incomplete #23

Closed nick-youngblut closed 3 years ago

nick-youngblut commented 3 years ago

panphlan requires Bowtie2 & Samtools, which are both on bioconda, but the panphlan bioconda recipe doesn't include these 2 softwares. Including both in the list of panphlan dependencies could help prevent conflicts among all panphlan dependencies, and the user doesn't have to install software outside of the panphlan recipe, which itself really doesn't fully install panphlan.

nick-youngblut commented 3 years ago

An example dependency conflict when trying to install bowtie2 & samtools after installing panphlan:

Looking for: ['bowtie2', 'samtools']

bioconda/linux-64        [====================] (00m:00s) No change
bioconda/noarch          [====================] (00m:00s) No change
pkgs/main/linux-64       [====================] (00m:00s) No change
r/linux-64               [====================] (00m:00s) No change
pkgs/main/noarch         [====================] (00m:00s) No change
pkgs/r/noarch            [====================] (00m:00s) No change
qiime2/linux-64          [====================] (00m:00s) No change
leylabmpi/noarch         [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change
r/noarch                 [====================] (00m:00s) No change
leylabmpi/linux-64       [====================] (00m:00s) No change
conda-forge/noarch       [====================] (00m:00s) Done
qiime2/noarch            [====================] (00m:00s) No change
conda-forge/linux-64     [====================] (00m:02s) Done
Encountered problems while solving.
Problem: package bowtie2-2.2.1-py38hed8969a_4 requires python >=3.8,<3.9.0a0, but none of the providers can be installed

panphlan only has the python requirement of python=3, but bowtie2 has more specific python version requirements.