MetaPhlAn Conda Install

[adamber1187]

Hi all,

Trying to use Humann2, but having trouble with installing MetaPhlAn. New to this world and trying to trouble shoot. Below is the error I'm getting when trying to install through Conda. Thanks for any help in advance.

(humann2) C:\Users\berlinba>conda install -c bioconda metaphlan2
WARNING conda.base.context:use_only_tar_bz2(632): Conda is constrained to only using the old .tar.bz2 file format because you have conda-build installed, and it is <3.18.3. Update or remove conda-build to get smaller downloads and faster extractions.
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

- metaphlan2 -> blast[version='>=2.6.0']
- metaphlan2 -> bowtie2[version='>=2.0.0']
- metaphlan2 -> muscle[version='>=3.8.1551']
- metaphlan2 -> pysam[version='>=0.8.3']
- metaphlan2 -> raxml[version='>=8.2.10']
- metaphlan2 -> samtools[version='>=0.1.19,<1.0']

Current channels:

- https://conda.anaconda.org/bioconda/win-64
- https://conda.anaconda.org/bioconda/noarch
- https://conda.anaconda.org/conda-forge/win-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/win-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/win-64
- https://repo.anaconda.com/pkgs/r/noarch
- https://repo.anaconda.com/pkgs/msys2/win-64
- https://repo.anaconda.com/pkgs/msys2/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

[Valentina Galata]

Am Montag, 15. Juli 2019 21:01:13 UTC+2 schrieb adamber1187:
> PackagesNotFoundError: The following packages are not available from current channels:

That is strange... I can install metaphlan2 using your command without any problems (conda version 4.7.5):

conda create -n test_metaphlan2
conda activate test_metaphlan2

conda install -c bioconda metaphlan2

Not sure whether this might be the issue but I would try to update your conda. You seem to have a pretty old version of it and I remember that I had some installation issues with an (less) old conda version which were resolved after the upgrade.

[adamber1187]

Thanks for the reply. I did update Conda (4.7.8), and still cannot install Metaphlan2 for some reason. Now getting this error:

C:\Users\berlinba>conda install -c bioconda metaphlan2

Collecting package metadata (repodata.json): done
Solving environment: failed

Initial quick solve with frozen env failed. Unfreezing env and trying again.
Solving environment: failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Package python conflicts for:
metaphlan2 -> python=2.7
Package matplotlib conflicts for:
metaphlan2 -> matplotlib
Package dendropy conflicts for:
metaphlan2 -> dendropy[version='3.12.3.*|3.12.3.*,>=3.12.3']
Package bowtie2 conflicts for:

metaphlan2 -> bowtie2[version='>=2.0.0']

Package pysam conflicts for:

metaphlan2 -> pysam[version='>=0.8.3']

Package msgpack-python conflicts for:
metaphlan2 -> msgpack-python
Package scipy conflicts for:
metaphlan2 -> scipy
Package numpy conflicts for:
metaphlan2 -> numpy=1.14.2
Package raxml conflicts for:

metaphlan2 -> raxml[version='>=8.2.10']

Package biom-format conflicts for:
metaphlan2 -> biom-format
Package requests conflicts for:
metaphlan2 -> requests
Package samtools conflicts for:

metaphlan2 -> samtools[version='>=0.1.19,<1.0']

Package biopython conflicts for:
metaphlan2 -> biopython
Package muscle conflicts for:

metaphlan2 -> muscle[version='>=3.8.1551']

Package pandas conflicts for:
metaphlan2 -> pandas=0.22
Package blast conflicts for:

[Valentina Galata]

Okay, now it is clear that there are version conflicts.
Ho did you create your environment? Did you install other packages before trying to install MetaPhlAn2?

[Francesco Beghini]

Hi Adam,

unfortunately, MetaPhlAn2 does not support any version of Windows and it is meant to be run exclusively on Linux. 

Best,

Francesco

Francesco Beghini

PhD Student - Laboratory of Computational Metagenomics

Department of Cellular, Computational and Integrative Biology - CIBIO

University of Trento

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[adamber1187]

Excellent, thanks a lot. Was able to download it on Linux. May be worth mentioning somewhere on the website that it is only Linux compatible since it isn't mentioned anywhere.

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