'module' object has no attribute 'bucky'

[yexiaying]

I have install bucky using conda as you inferred in 'Cookbook for running BUCKy in parallel in a Jupyter notebook' and import it, but I still got the error informattion import ipyrad as ip import toytree import ipyrad.analysis as ipa import ipyparallel as ipp ipyclient = ipp.Client()

c = ipa.bucky(name="buckytest", data="/ds3200_1/users_root/lidezhu/yexiaying/newassembly/alldata_outfiles/alldata.loci", workdir="analysis-bucky", samples=samples, minsnps=0, )

AttributeErrorTraceback (most recent call last)

in () ----> 1 c = ipa.bucky(name="buckytest", 2 data="/ds3200_1/users_root/lidezhu/yexiaying/newassembly/alldata_outfiles/alldata.loci", 3 workdir="analysis-bucky", 4 samples=samples, 5 minsnps=0, AttributeError: 'module' object has no attribute 'bucky' What do you think the cause of this problem?

[isaacovercast]

ipyrad version?

Something is wrong with your install or you are using an old version. Did you try reinstalling?

[ricoperdiz]

I'm having similar issue. I've tried reinstalling, also did a fresh install. My ipyrad version now is 0.6.27. When I try to run conda install -c ipyrad bucky, I receive the following message:

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

  - bucky

Any idea?

[isaacovercast]

Update to the newest version of ipyrad (0.7.30) conda install -c ipyrad ipyrad -f. What happens if you try this?

[ricoperdiz]

I've just seen on gitter that it looks like that OSX version is not available yet. And I'm running on Mac OS X. I forgot telling you this.

Anyway, I tried and, as expect after reading gitter messages, it remained on version 0.6.27.

Thank you.

R.

[isaacovercast]

OSX version should be up to date: [image: image.png]

What did you try exactly and what was the exact result?

On Fri, Jul 12, 2019 at 10:11 PM Ricardo Perdiz notifications@github.com wrote:

I've just seen on gitter that it looks like that OSX version is not available yet. And I'm running on Mac OS X. I forgot telling you this.

Anyway, I tried and, as expect after reading gitter messages, it remained on version 0.6.27.

Thank you.

R.

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[ricoperdiz]

Hi,

First, I tried updating conda, then updating ipyrad through commands below:

conda update conda
conda install -c ipyrad ipyrad

It did not work.

Then you proposed to force update using option -f. It also did not work.

Then I decided to remove miniconda from my computer, and make a new fresh install.

So I followed instructions from https://ipyrad.readthedocs.io/installation.html. The result was that I was not able to install ipyrad. I got the following error message:

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

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

  - ipyrad -> mpi4py

Current channels:

  - https://conda.anaconda.org/ipyrad/osx-64
  - https://conda.anaconda.org/ipyrad/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/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.

Any guess?

[isaacovercast]

The conda install failed because of a missing dependency (mpi4py). I fixed this and tested it so the conda install -c ipyrad ipyrad should work now.

[isgilman]

Hello all,

I know this is late, but I'm also having trouble finding the bucky conda package. I tried the steps above (force reinstall of ipyrad). I'm currently working with

ipyrad                    0.9.54             pyh9f0ad1d_0    bioconda

and see the package on Anaconda Cloud, but can't find it when trying to install:

$ conda install -c ipyrad bucky
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

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

  - bucky

Current channels:

  - https://conda.anaconda.org/ipyrad/osx-64
  - https://conda.anaconda.org/ipyrad/noarch
  - https://public.dhe.ibm.com/ibmdl/export/pub/software/server/ibm-ai/conda/osx-64
  - https://public.dhe.ibm.com/ibmdl/export/pub/software/server/ibm-ai/conda/noarch
  - https://conda.anaconda.org/bioconda/osx-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/daler/osx-64
  - https://conda.anaconda.org/daler/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/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.

I've attached the environment information from conda info and conda list here: phylo.conda.list.txt.

Thanks, Ian

[isaacovercast]

There is only a linux build of bucky in the ipyrad conda repo. I am guessing you are on mac? If you install bucky by hand the ipyrad bucky analysis tool will find it.

[isgilman]

Ah, thanks Isaac, I misinterpreted your comment about the OS X update above. I'll try installing bucky from source and working it into ipyrad.

Thank you!