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Question about installation #28

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Yansr3 opened this issue Aug 23, 2023 · 12 comments
Open

Question about installation #28

Yansr3 opened this issue Aug 23, 2023 · 12 comments

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@Yansr3
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Yansr3 commented Aug 23, 2023

I'm trying to create a mira environment following the steps in Getting Started. I'm using a M1 macos system. I tried with both python 3.11 and python 3.10, but both didn't work. May I ask for any help or suggestions on setting up the environment?

conda create --name mira-env -c conda-forge -c bioconda scanpy jupyter leidenalg
conda activate mira-env
conda install -c bioconda mira-multiome

But I'm getting this Unsatisfiable Error.
(mira-env) ➜ ~ conda install -c bioconda mira-multiome
Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

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

Output in format: Requested package -> Available versions
@Yansr3
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Yansr3 commented Aug 23, 2023

I also tried to install with pip. But I got another conflict error.
ERROR: Cannot install mira-multiome==0.0.0, mira-multiome==0.0.1, mira-multiome==0.0.2, mira-multiome==0.0.3, mira-multiome==0.0.4, mira-multiome==0.0.5, mira-multiome==0.0.6, mira-multiome==0.0.7, mira-multiome==0.0.8, mira-multiome==0.0.9, mira-multiome==0.1.0, mira-multiome==0.1.3, mira-multiome==1.0.0, mira-multiome==1.0.1, mira-multiome==1.0.2, mira-multiome==1.0.3, mira-multiome==1.0.4 and mira-multiome==2.1.0 because these package versions have conflicting dependencies.

The conflict is caused by:
mira-multiome 2.1.0 depends on torch<2 and >=1.8.0
mira-multiome 1.0.4 depends on torch<2 and >=1.8.0
mira-multiome 1.0.3 depends on torch<2 and >=1.8.0
mira-multiome 1.0.2 depends on torch<2 and >=1.8.0
mira-multiome 1.0.1 depends on torch<2 and >=1.8.0
mira-multiome 1.0.0 depends on torch<2 and >=1.8.0
mira-multiome 0.1.3 depends on torch<2 and >=1.8.0
mira-multiome 0.1.0 depends on torch<2 and >=1.8.0
mira-multiome 0.0.9 depends on torch<2 and >=1.8.0
mira-multiome 0.0.8 depends on torch<2 and >=1.8.0
mira-multiome 0.0.7 depends on torch<2 and >=1.8.0
mira-multiome 0.0.6 depends on torch<2 and >=1.8.0
mira-multiome 0.0.5 depends on torch<2 and >=1.8.0
mira-multiome 0.0.4 depends on torch<2 and >=1.8.0
mira-multiome 0.0.3 depends on torch<2 and >=1.8.0
mira-multiome 0.0.2 depends on torch<2 and >=1.8.0
mira-multiome 0.0.1 depends on torch<2 and >=1.8.0
mira-multiome 0.0.0 depends on torch<2 and >=1.8.0

@AllenWLynch
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AllenWLynch commented Aug 24, 2023 via email

@Yansr3
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Yansr3 commented Aug 24, 2023

Hi AL,

Thanks for responding. I tried with python 3.9 but neither conda nor pip install worked. I also tried python 3.5 to python 3.8, but they didn't work.

SY

@AllenWLynch
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AllenWLynch commented Aug 25, 2023 via email

@AllenWLynch
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Found the issue, now I am confirming that install works under more conditions. Today, I will submit pull requests to Bioconda to update the MIRA package dependencies, which will likely be ready tomorrow.

@Yansr3
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Yansr3 commented Aug 29, 2023

Thank you very much! I will try installing from bioconda tomorrow.

@AllenWLynch
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The issue was that the fast motif calling software I dependent on, MOODS, had some C compiler options which were not compatible on M1 Mac. The maintainer has not responded to an issue on this topic from three months ago, so I am fixing the compiler issues and distributing my own version. I need one more day to put it together, sorry for the inconvenience.

@Yansr3
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Yansr3 commented Aug 30, 2023

No worries, thank you very much for helping with this! I will wait and try again when it's ready.

@Yansr3
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Yansr3 commented Aug 30, 2023

Sorry this may be another question, but I want to quickly ask if it is possible to use GPU after I install mira into M1 Mac.

@AllenWLynch
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AllenWLynch commented Sep 7, 2023 via email

@AllenWLynch
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Hi, an update on running MIRA on python 3.10 and 3.11 systems. The bioconda team is being very sluggish approving my PRs still, but you can access a new alpha version for 3.10 and 3.11 on PyPi. To set up an env, run:

conda create --name mira-3.11 -c conda-forge -c bioconda scanpy jupyterlab ipywidgets seaborn
conda activate mira-3.11
pip install mira-multiome==2.1.1a3

This will undergo a bit more testing before full release. I have no idea how long it will take to get this hosted on Bioconda.

@Yansr3
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Yansr3 commented Sep 11, 2023

Hi, thank you very much for the updating! I succesfully installed with pip on python 3.9. I will also try on python 3.10 with the alpha veriosn.

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@AllenWLynch @Yansr3