Can't install Nanosim

[aerusakovich]

Hello! I am having troubles with installation. Could you help pls? System: Mac OS X Version 14.2.1 (23C71)

Installation in conda

(nanosim) anastasia@Anastasias-MBP NanoSim % conda install -c bioconda -c conda-forge nanosim            
Channels:
 - bioconda
 - conda-forge
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides htseq needed by nanosim-2.0.0-pyr341h24bf2e0_1

Could not solve for environment specs
The following packages are incompatible
└─ nanosim is not installable because there are no viable options
   ├─ nanosim [2.0.0|2.1.0] would require
   │  └─ htseq, which does not exist (perhaps a missing channel);
   ├─ nanosim [2.2.0|2.5.0|2.5.1|2.6.0|3.0.0] would require
   │  └─ htseq >=0.9.1 , which does not exist (perhaps a missing channel);
   └─ nanosim [3.0.2|3.1.0] would require
      └─ genometools-genometools, which does not exist (perhaps a missing channel).

Tried installing missing packages with Homebrew and pip, while in the same conda env, yet didn't help:

nanosim) anastasia@Anastasias-MBP NanoSim % brew install genometools
==> Downloading https://formulae.brew.sh/api/formula.jws.json
######################################################################### 100.0%
==> Downloading https://formulae.brew.sh/api/cask.jws.json
######################################################################### 100.0%
Warning: genometools 1.6.5 is already installed and up-to-date.
To reinstall 1.6.5, run:
  brew reinstall genometools

  (nanosim) anastasia@Anastasias-MBP NanoSim % pip install HTSeq             
Collecting HTSeq
  Using cached HTSeq-2.0.5-cp312-cp312-macosx_11_0_arm64.whl
Collecting numpy (from HTSeq)
  Using cached numpy-1.26.4-cp312-cp312-macosx_11_0_arm64.whl.metadata (61 kB)
Collecting pysam (from HTSeq)
  Using cached pysam-0.22.0-cp312-cp312-macosx_11_0_arm64.whl.metadata (1.5 kB)
Using cached numpy-1.26.4-cp312-cp312-macosx_11_0_arm64.whl (13.7 MB)
Using cached pysam-0.22.0-cp312-cp312-macosx_11_0_arm64.whl (8.0 MB)
Installing collected packages: pysam, numpy, HTSeq
Successfully installed HTSeq-2.0.5 numpy-1.26.4 pysam-0.22.0

(nanosim) anastasia@Anastasias-MBP NanoSim % conda install -c bioconda -c conda-forge nanosim
Channels:
 - bioconda
 - conda-forge
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides htseq needed by nanosim-2.0.0-pyr341h24bf2e0_1

Could not solve for environment specs
The following packages are incompatible
└─ nanosim is not installable because there are no viable options
   ├─ nanosim [2.0.0|2.1.0] would require
   │  └─ htseq, which does not exist (perhaps a missing channel);
   ├─ nanosim [2.2.0|2.5.0|2.5.1|2.6.0|3.0.0] would require
   │  └─ htseq >=0.9.1 , which does not exist (perhaps a missing channel);
   └─ nanosim [3.0.2|3.1.0] would require
      └─ genometools-genometools, which does not exist (perhaps a missing channel).

Installation with mamba

(nanosim_env) anastasia@Anastasias-MBP NanoSim % micromamba install scikit-learn=0.22.1 six samtools pysam pybedtools minimap2 joblib htseq genometools-genometools
pkgs/r/osx-arm64 (check zst)                       Checked  0.1s
pkgs/r/noarch (check zst)                          Checked  0.1s
pkgs/main/osx-arm64 (check zst)                    Checked  0.1s
pkgs/main/noarch (check zst)                       Checked  0.1s
pkgs/r/osx-arm64                                   108.0 B @   2.8kB/s  0.0s
pkgs/main/noarch                                   705.1kB @   7.4MB/s  0.1s
pkgs/main/osx-arm64                                  2.3MB @  11.2MB/s  0.2s
pkgs/r/noarch                                        2.1MB @   9.8MB/s  0.2s
error    libmamba Could not solve for environment specs
    The following packages are incompatible
    ├─ genometools-genometools does not exist (perhaps a typo or a missing channel);
    ├─ htseq does not exist (perhaps a typo or a missing channel);
    ├─ minimap2 does not exist (perhaps a typo or a missing channel);
    ├─ pybedtools does not exist (perhaps a typo or a missing channel);
    ├─ pysam does not exist (perhaps a typo or a missing channel);
    ├─ samtools does not exist (perhaps a typo or a missing channel);
    └─ scikit-learn 0.22.1**  does not exist (perhaps a typo or a missing channel).
critical libmamba Could not solve for environment specs

Installation from requirements:

(nanosim_env) anastasia@Anastasias-MBP NanoSim % conda install --file requirements.txt -c conda-forge -c bioconda
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

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

  - scikit-learn==0.22.1
  - pysam==0.15.3
  - pybedtools==0.8.1
  - minimap2==2.17
  - htseq==0.11.3
  - samtools
  - last
  - genometools-genometools

Current channels:

  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/bioconda
  - defaults

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.

[lcoombe]

Hi @aerusakovich,

Currently, bioconda packages are not built for osx-arm64 architecture. There is additional information here: https://github.com/bioconda/bioconda-recipes/issues/45586

You could try the workaround described in that issue, or use an alternate approach, such as utilizing the quay.io docker image (https://quay.io/repository/biocontainers/nanosim?tab=info).

I hope that helps - thank you for your interest in NanoSim! Lauren

[aerusakovich]

Thank you!