Picrust2 Installation in Mac M1

[Misbah Tubassam]

Hey Picrust2 community, I hope you all are doing great. I am trying to install Picrust2 on M1. I have tried using Conda, Anaconda, and Mamba, and none seems to be working. I have tried each and every solution available already in this community, like one by Robyn https://groups.google.com/g/picrust-users/c/HWoAC6wMYdc or anywhere else on the internet. I have tried versions 2.5.3, 2.5.2, and 2.5.1, but unfortunately, no success. I preinstalled dendropy in my environment, essentials, etc., but still it's not getting solved. I don't have any background in computer science, so these things are quite complicated for me. Please help me out to troubleshoot it and for successful installation. Below I am attaching the error I was getting. This error contains dendropy as well, but later on I installed dendropy but still the remaining errors were the same. I think there is some error related to pango and Conda Fonts ecosystem, and the other one is that Python 3.10 is not installable due to missing tzdata. I have tried installing tzdata 22024b as well, but it didn't resolve the issue.

Thank you in advance.

[Misbah Tubassam]

To make it more clear, I want to mention that before, my operating system was monetary 12.xx and I had installed Picrust2 and used it for my datasets. But now my operating system is upgraded to Sonoma 14, and now I am unable to install Picrust 2, and I have tried every possible solution as per my understanding and available here in this community and on other platforms. Could it be related to that?

Please help me to figure out the issue. Thank you in advance.

Regards:

Misbah Tubassam 

[Misbah Tubassam]

Hey, to make it more clear, I want to mention that earlier I had a monetary 12.x operating system and installed and used Picrust2 for my datasets. But after updating my operating system to Sonama 14.x, now I am unable to install Picrust 2. I have tried each and every solution for this, but nothing is working for me. Please help me to figure out this issue. Thank you in advance.

Regards:

Misbah Tubassam

On Monday, January 6, 2025 at 6:48:32 PM UTC+5 Misbah Tubassam wrote:

[Robyn Wright]

Hi Misbah,

Can you please send all of the commands that you are running, including creating and activating the environment? 

Thanks,

Robyn

[Misbah Tubassam]

Hi Robyn,

Thank you so much for your reply. Below are the commands I am using to install Picrust2.

wget https://github.com/picrust/picrust2/archive/v2.5.3.tar.gz
tar xvzf  v2.5.3.tar.gz
cd picrust2-2.5.3/

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add subdirs osx-64

conda env create -f picrust2-env.yaml -n picrust-v2.5.3_2
conda activate picrust-v2.5.3_2
pip install --editable .
conda install r-essentials

I have been using this code, and I have tried to install it in a separate environment with Python 3.7, 3.8, and 3.9 and also in the base environment with Python 3.12.  I have tried in Anaconda, Miniconda, and Miniforge, but unfortunately nothing worked. conda env create -f picrust2-env.yaml -n picrust-v2.5.3_2 environment creation was not successful; every time it just failed with the error that I have attached above. 

Every time I tried in a freshly created environment or freshly installed conda.

Thanks,

Misbah

[Robyn Wright]

Apologies for the slow reply. I've been working on a new database and a new release of PICRUSt2 at the moment and am currently trying to work on testing out the installation on my own Mac laptop but have been having issues with conda more generally. I just wanted to give you an update that I'm still looking into this and will update when I have fixed the issues for myself and can test more thoroughly!

Thanks,

Robyn

[Robyn Wright]

I wasn't expecting to update this so quickly! I think that I was having a similar issue, but adding --platform osx-64 to the environment creation command seemed to work. 

So try running:

wget https://github.com/picrust/picrust2/archive/v2.5.3.tar.gz
tar xvzf  v2.5.3.tar.gz
cd picrust2-2.5.3/

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add subdirs osx-64

conda env create --platform osx-64 -f picrust2-env.yaml -n picrust-v2.5.3_2

conda activate picrust-v2.5.3_2
pip install --editable .
conda install r-essentials

[Misbah Tubassam]

Hey Robyn, 

Thank you so much for the quick follow-ups and for sharing the changed scripts! I really appreciate the effort you’ve put into resolving this. It’s great to hear that adding platform osx-64 to the environment creation command worked for you. I’ll give the updated commands a try on my end and see how things go.  Once I’ve had a chance to test everything, I’ll be sure to update you. Thanks again for your help and the clear instructions!

Regards:

Misbah

[Misbah Tubassam]

Hey Robyn,

 Thanks again for your support and the updated commands. I’ve tried running the changed commands, but unfortunately, it’s still not working for me. I’m encountering the same error, and the environment is not being created as expected.

Would you be able to suggest any further steps or potential solutions? Any additional guidance would be greatly appreciated.

Thanks again for all your help, and I look forward to hearing from you!

Best regards,
Misbah

[Robyn Wright]

Oh that is really annoying. It's difficult to troubleshoot without being able to reproduce the error. My best suggestion at the moment is either to wait for me to have finished creating the update to PICRUSt2 (I'm not sure if that will help, though), or to use the plugin version of PICRUSt2 that can be installed with QIIME2. You can find the instructions for that here - note that they assume that you already have an environment installed with QIIME2. The plugin does have slightly reduced functionality, but will be adequate for most users.

Robyn

[Chathuranga De Silva]

Hello Robyn,

I tried the code you suggested, and this is what I got.

I'm not using Picrust2 anymore. Just thought of sharing this with you, so that you can have a look at.

Please see the attached file.

Model Name: MacBook Pro

  Model Identifier: Mac15,6

  Model Number: MRX33LL/A

  Chip: Apple M3 Pro

  Total Number of Cores: 11 (5 performance and 6 efficiency)

  Memory: 18 GB

  System Firmware Version: 11881.41.5

  OS Loader Version: 11881.41.5

Graduate Research Assistant,

Agronomy and Plant-Microbial Interactions

Department of Agricultural, Food and Nutritional Science

4-65 Agriculture/Forestry Centre

University of Alberta

Edmonton, AB, T6G 2P5

Tel: 780.909.8920

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[Simran Patel]

Hi all,

I have a Macbook Pro (M3 silicon) and have encountered this exact same issue with dendropy, tzdata, and fonts-conda-ecosystem. None of the forum solutions have worked. I look forward to seeing if we can find a solution.

[Simran Patel]

Hi all,

I do not know if my previous message has gone through but I have the exact same issue as OP with installing PICRUSt2 - I have attached my code here. I have a Macbook Pro running M3 silicon. The only difference is I installed miniconda with osx-64 hardware in the first place (all I get is a warning about the different architecture, but all other conda commands works as normal. Only the environment creation step breaks down.)

Look forward to hearing about potential solutions.

p.s. I am currently trying to install a conda environment with version 2.5.2 but it is taking quite a while. The same happened with version 2.5.1. 

[Robyn Wright]

Hi there,

Thanks for the additional info everyone. I think there are some different things going on - @bacdesilva, I think that you are trying to install PICRUSt2 into an existing environment. I recommend removing the unsuccessful installs or creating a new environment with a different name.

@Simran, please try running with the code that I gave above that includes the platform option (that's not in the output that you sent, so I assume it's not what you ran):

wget https://github.com/picrust/picrust2/archive/v2.5.3.tar.gz
tar xvzf  v2.5.3.tar.gz
cd picrust2-2.5.3/

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add subdirs osx-64

conda env create --platform osx-64 -f picrust2-env.yaml -n picrust-v2.5.3_2

conda activate picrust-v2.5.3_2
pip install --editable .
conda install r-essentials

Please also note that you will also need to make sure that there either isn't an existing environment called picrust-v2.5.3_2, or you will need to change this name. 

Also, if any of you are interested, I am about to release a new version of PICRUSt2 with a new database. You can see some details on it, including installation instructions, here. You will likely still need to add the --platform osx-64 command to the environment creation step. 

My Mac is an M1, so I'm not able to check whether the issues you're having are specific to an M3 laptop, but given that they are similar to those originally mentioned, I assume not. I'll also note that I've recently had issues with conda more generally on my Mac (this seems to happen regularly with OS updates) - it could be that re-installing conda will help to fix some of the problems you're running into. 

Robyn

[Robyn Wright]

Hi all,

I've been investigating this slightly more and I think that the issue is that the version of SEPP that is required here requires a version of dendropy that isn't available for Mac. Installation for me does still work with the following:

1. wget https://github.com/picrust/picrust2/archive/v2.6.0.tar.gz
2. tar xvzf  v2.6.0.tar.gz
3. cd picrust2-2.6.0/

4. conda env create -n picrust2-2.6.0-github -f picrust2-env.yaml --platform osx-64

5. conda activate picrust2-2.6.0-github
6. pip install --editable .

7. pytest

If this still isn't working for you, I'd recommend:

• Carry out steps 1-3
• Edit the picrust2-env.yaml file and remove the sepp, r-castor, hmmer, epa-ng & dendropy lines completely
• Run steps 4-5
• Install r-essentialy, sepp, r-castor, hmmer, epa-ng and dendropy separately (into the picrust2 environment, either using conda/pip or from source as their own Github pages direct)
• Run steps 6-7

Robyn

[Misbah Tubassam]

Hey Robyn,  

Thank you for getting back to us and dedicating your time and efforts to resolve the issue. I had earlier tried by editing the yaml file but at that time it didn't work. But I'll surely try this again with picrust2 updtaed version and your recommendations. I'm hopeful that it would work out.

Will get back to you soon after trying this out.

Regards :

Misbah

To view this discussion visit https://groups.google.com/d/msgid/picrust-users/6c88e0e7-ed00-488d-826b-fe5d8493a509n%40googlegroups.com.

[Simran Patel]

Thankyou so much! I have installed the relevant packages using the .tar.bz files on the Anaconda website. However, when I run pytest, I get so many errors that pytest aborts itself. Attached is my last few package installations and my attempt at running steps 6-7. I have also put my conda environment package list here so you can see if there are any version or source errors.

[Robyn Wright]

Hmm OK, everything looks like it's the right version. Could you try running the scripts inside the tests folder individually? I'm wondering if that would give slightly more informative error messages than with pytest. 

Robyn

[Simran Patel]

Thankyou for replying so quickly. The error I get is ModuleNotFoundError: No module named 'picrust2'. I can only find information to solve this error using the QIIME plugin, but I can't even get QIIME to work (which is an issue for another day). Would there be a reason this shows up in a native installation?

[Simran Patel]

Adding context in case it is useful in the future

I downloaded the packages using files of the relevant versions from Anaconda, for example:

https://anaconda.org/etetoolkit/ete3/files

https://anaconda.org/bioconda/sepp/files

And then used conda install Downloads/<file name>.tar.bz

[Robyn Wright]

That error message I believe is referring to it not being able to find the picrust2 folder containing scripts that are called from the test scripts, which suggests that something didn't go right with the install as those should be findable. Could you try removing the PICRUSt2.egg-info folder and then maybe try running the install with this command instead?: pip install --use-pep517 --config-settings editable_mode=compat -e .

Robyn

[Simran Patel]

Thankyou for your support. I tried re-installing conda and going through everything from scratch, and added the modification to step 6 you suggested. Looking into the error more deeply, it seems the file "libffi.6.dylib" is missing from the conda environment (I checked the lib folder and indeed there is no such file). This is causing the error for all test files - more specifically "Library not loaded: @rpath/libffi.6.dylib". 

[Simran Patel]

Hello, has anyone had any luck installing PICRUSt2 since this thread was last updated? I am still getting the same error as two weeks ago.

[Robyn Wright]

This looks like a conda issue and not a PICRUSt2 issue.... could you try following some of the suggested fixes here?

Robyn

[Misbah Tubassam]

Hey Simran, same here, no luck. 

To view this discussion visit https://groups.google.com/d/msgid/picrust-users/c3a4decf-9858-44ce-981a-fe35beb448ecn%40googlegroups.com.

[Simran Patel]

Thankyou for your reply. I have removed and reset everything and started from scratch - conda now works as expected. Here is the output I get from step 5 onwards (environment already created). I'm back to the "no module found: picrust2" problem from earlier, so clearly the new installation command did not work and I've gone in a circle.

[Robyn Wright]

Hi,

The output still appears to be saying that PICRUSt2 is installed before you are running the install command. Can you please show the entire output, from where you create a new conda environment, download PICRUSt2, install any other dependencies, etc? 

Thanks,

Robyn

[Simran Patel]

Thankyou Robyn! That was indeed the case, so I looked further into the installation outputs and it turns out there was some files stored in ~/Library from previous installations which must have been causing confusion. Here's what I did:

• Removed basically the entire ~/Library/Python/3.9 directory
• Recursively removed miniconda3 and picrust2 folders
• Removed miniconda3 and picrust2 from the PATH variable, as that was there from previous installations
• Reinstalled miniconda3 and picrust2 from scratch using the 7 steps from earlier

Finally I have a working PICRUST2 (or at least so far, two steps into the tutorial).

Thankyou so much for your support and perseverance, answering all my silly questions! I really appreciate it.

[Robyn Wright]

I am so glad that this (finally) worked for you, and thanks for sharing the steps that worked - hopefully they'll help others!

Robyn