Problem installing ipyrad on ubuntu

[kbkinsey]

Hi there -

I installed and used ipyrad before on my lab's ubuntu computer, but I went back to branch at step 7 and apparently ipyrad is no longer installed on the machine. I went to go re-install ipyrad using the resources at the pages below and none of these install methods are working.

When I run "conda install -c bioconda ipyrad" it gets stuck on solving the environment. It says "failed with initial frozen solve. Retrying with flexible solve"... Then that fails too... I've tried workaround for the past 2 hrs and nothing will do.

Any help is appreciated.

Thanks.

[isaacovercast]

Hi Kinsey,

Did you try including the conda-forge channel? conda install -c conda-forge -c bioconda ipyrad, that's the recommended install command. If you still have problems being stuck solving the environment you can try swapping out the default solver for the libmamba solver. You can see the commands to do this on the ipyrad install docs page: https://ipyrad.readthedocs.io/en/master/3-installation.html#fixing-conda-install-stuck-on-solving-environment

Let me know how it goes. -isaac

[khorikhori]

Good morning, Isaac, Error occurred even libmanda is installed in Ubuntu 20.

$ conda update -n base conda $ conda install -n base conda-libmamba-solver $ conda config --set solver libmamba

No problems above. But...

$ conda install -c conda-forge -c bioconda ipyrad

Channels:

• conda-forge
• bioconda
• defaults Platform: linux-64 Collecting package metadata (repodata.json): done Solving environment: / warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• package ipyrad-0.9.10-py_0 requires pysam >=0.15, but none of the providers can be installed

Could not solve for environment specs The following packages are incompatible tq ipyrad is installable with the potential options x tq ipyrad [0.9.10|0.9.11|...|0.9.93] would require x x mq pysam >=0.15 with the potential options x x tq pysam [0.15.0|0.15.0.1|...|0.20.0] would require x x x mq python >=2.7,<2.8.0a0 , which can be installed; x x tq pysam [0.15.0|0.15.0.1|0.15.1|0.15.2] would require x x x mq python >=3.5,<3.6.0a0 , which can be installed; x x tq pysam [0.15.0|0.15.0.1|...|0.21.0] would require x x x mq python >=3.6,<3.7.0a0 , which can be installed; x x tq pysam [0.15.2|0.15.3|...|0.21.0] would require x x x mq python >=3.7,<3.8.0a0 , which can be installed; x x tq pysam [0.15.2|0.16.0.1|...|0.22.0] would require x x x mq python >=3.8,<3.9.0a0 , which can be installed; x x tq pysam [0.16.0.1|0.17.0|...|0.22.0] would require x x x mq python >=3.9,<3.10.0a0 , which can be installed; x x mq pysam [0.19.1|0.20.0|0.21.0|0.22.0] would require x x mq python >=3.10,<3.11.0a0 , which can be installed; x mq ipyrad 0.9.7 would require x mq python 2.7. , which can be installed; mq pin-1 is not installable because it requires mq python 3.11. , which conflicts with any installable versions previously reported.

Pins seem to be involved in the conflict. Currently pinned specs:

• python 3.11.* (labeled as 'pin-1')

Any help is appreciated.

Thank you very much.

[isaacovercast]

This is a downstream error coming from bioconda not yet supporting python 3.11 builds. You can install ipyrad if you force python 3.10 in the conda environment: conda create -n ipyrad python=3.10; conda activate ipyrad

[khorikhori]

Dear Mr. Issac, Thank you very much for your suggestion. 30 minitues ago, I solved this problem by following methods.

1) Anaconda is not necessary for installation of ipyrad. 2) Just install miniconda 3 $ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh $ bash Miniconda3-latest-Linux-x86_64.sh $ source ~/.bashrc 3) conda create -n ipyrad conda activate ipyrad conda install ipyrad -c conda-forge -c bioconda 4) The 'libmamba problem' was not occurred in this method.

I'd like to test later whether the installed ipyrad run well.

[isaacovercast]

Hello, Ok great, glad you got it installed and thank you for sharing the installation instructions. The libmamba problem doesn't occur anymore because in the latest version of miniconda libmamba has been set to the default solver, which is very useful. Good luck!