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M2 MacOS Installation Troubles #282

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keenajm1 opened this issue Aug 20, 2023 · 8 comments
Open

M2 MacOS Installation Troubles #282

keenajm1 opened this issue Aug 20, 2023 · 8 comments

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@keenajm1
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Hello,

I'm sorry for posting yet another installation troubleshooting request, but I've tried browsing the solved and unsolved issue boards and still just can't find a solution.

My Mac has an M2 Max Chip and I therefore tried to install the biostars software with the newest version of x86_64 miniconda3, which I installed via the script. (I should note here that I have tried to install the software like 3 different times using Anaconda and miniconda, both ARM and x86_64). It would seem that regardless of what iteration of conda I choose, I can't install the biostars software.

I believe I have been going through the prerequisite steps appropriately, but when I use the installation script, I get arrested at step 4/10, where the terminal outputs the error I have attached below:

Screenshot 2023-08-20 at 5 21 30 PM

I have also tried downloading both samtools and htslib directly via conda install samtools/htslib. It doesn't seem to do much, as I can see that they are both downloaded, but I still get the same error. I have also tried downloading the most recent versions of both that are mentioned in the prompt (1.17), but it leads to further version conflicts with libdeflate, libzlib, and lib.

I do suffer from some computer science illiteracy and the fact that I've done this several times has muddled things together, but I do know for certain that no matter what I've done, I've been stopped at step 4 with the claim of these packages being an issue.

On a side note, on my most recent installation using miniconda, I'm struggling with permission issues. I got a permission issue in step 3, and I can't activate the "bioconda" environment. I was able to in past tries. This permission issue is a real annoyance, as I can't download base r from the console anymore. I have had to use sudo conda install on my most recent attempt to install samtools and htslib, which doesn't seem proper.

Anyways, I apologize for piling on with another troubleshooting issue. If the answer is I simply need to be patient since these M2 chips are very new, I understand. I want to dive into the biostars material, but I can't even get myself to square one. Any help is greatly appreciated and thank you for taking the time!
@ialbert
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ialbert commented Aug 21, 2023

The ever-changing Mac platforms are a problem.

I have recently (as in a few days ago) rewritten the installation instructions to use micromamba installer.

Micromamba is a standalone variant of conda/mamba that is more robust.

Give micromamba a go but always use the Intel x86_64 version of it. Bioinformatics software is only compiled for Intel and always needs to be run in emulation.

This week a cohort of new students will go through the book and as such the various pitfalls will come out and hopefully get correct.

@Meshesha78
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Hi, same problem here with a similar error message. Fortunately, I have a Windows PC and working ok with Ubuntu. Let me know if you solve it.

Thanks,

Mes

@ialbert
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ialbert commented Jan 3, 2024 •
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We went through the installation with a cohort of 30 students. Half had fairly new Apple laptops.

In all cases where we had troubles (and that was about 3 people), the problem was always that installation instructions were not followed strictly or that the student already had another version of conda (sometimes anaconda or miniconda) already installed.

Make sure to activate bash, install the dependencies on MacOS, and so on.

Installing micromamba is not bioinformatics-related task and as far as I know, tens of thousands of people use it successfully on M2. Basically what I am saying here is that to best of my knowledge it works well.

@Meshesha78
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Thanks a lot,
I see the problem. I have anaconda3 already installed which may be creating the problem. Will remove it and try again.
Thanks again

Mes

@ialbert
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ialbert commented Jan 3, 2024

if you have anaconda you might want to try using that instead of micromamba it might work,

or start invoking micromamba directly to bypass the existing setup, invoke it as:

~/bin/micromamba

these tools are very similar but can compete with one another

@Meshesha78
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Meshesha78 commented Jan 3, 2024 via email

@ialbert
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ialbert commented Jan 3, 2024 •
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You have installed the incorrect version of micromamba, make sure to follow the manual.

You have to install the Intel based micromamba even on the M1 processor.

It will work seamlessly and just fine. Bioinformatics software is available only for Intel based Macs and will run in emulation mode on M1.

You will need to uninstall then follow the book closely.

curl http://data.biostarhandbook.com/uninstall.sh | bash

then do the installation again

@Meshesha78
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Meshesha78 commented Jan 4, 2024 via email

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3 participants
@ialbert @Meshesha78 @keenajm1