Library Issue

[utkarsh027]

There is a issue regarding library conflict. So please can You rerun the sctiger and let me know the exact cause of error, after inflating the data step.

[chenyongrowan]

Hi! Can you please send the list of packages installed for your scTIGER environment? If you installed scTIGER using the installation instructions in our README.md file, you can get this by typing conda list -n scTIGER.

Some of the packages may have been updated. We provide the version for each package on our installation in the prerequisites section of our README.md file. If you specify each package to match the version we are using, it should run without error.

[utkarsh027]

Ok i will do it today

On Mon, Apr 29, 2024 at 8:16 AM chenyongrowan @.***> wrote:

Hi! Can you please send the list of packages installed for your scTIGER environment? If you installed scTIGER using the installation instructions in our README.md https://github.com/chenyongrowan/scTIGER/blob/main/README.md file, you can get this by typing conda list -n scTIGER.

Some of the packages may have been updated. We provide the version for each package on our installation in the prerequisites section of our README.md https://github.com/chenyongrowan/scTIGER/blob/main/README.md file. If you specify each package to match the version we are using, it should run without error.

— Reply to this email directly, view it on GitHub https://github.com/chenyongrowan/scTIGER/issues/1#issuecomment-2083014065, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMQX3RUJPT6UBFDC5KXFYQLY7ZP5JAVCNFSM6AAAAABGYFZ2WGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBTGAYTIMBWGU . You are receiving this because you authored the thread.Message ID: @.***>

[utkarsh027]

I used same packages as in Readme but there was conflict between numpy and bambi

On Mon, Apr 29, 2024 at 10:27 AM Utkarsh Tiwari < @.***> wrote:

Ok i will do it today

On Mon, Apr 29, 2024 at 8:16 AM chenyongrowan @.***> wrote:

Hi! Can you please send the list of packages installed for your scTIGER environment? If you installed scTIGER using the installation instructions in our README.md https://github.com/chenyongrowan/scTIGER/blob/main/README.md file, you can get this by typing conda list -n scTIGER.

Some of the packages may have been updated. We provide the version for each package on our installation in the prerequisites section of our README.md https://github.com/chenyongrowan/scTIGER/blob/main/README.md file. If you specify each package to match the version we are using, it should run without error.

— Reply to this email directly, view it on GitHub https://github.com/chenyongrowan/scTIGER/issues/1#issuecomment-2083014065, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMQX3RUJPT6UBFDC5KXFYQLY7ZP5JAVCNFSM6AAAAABGYFZ2WGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBTGAYTIMBWGU . You are receiving this because you authored the thread.Message ID: @.***>

[chenyongrowan]

I see what happened. Pytorch released new versions and it is forcing certain packages to update which becomes incompatible with Bambi. I was just able to install scTIGER on my CPU processing machine with the following commands:

conda create -n scTIGER python=3.9.2 conda activate scTIGER conda install pytorch==2.1.2 torchvision==0.16.2 torchaudio==2.1.2 cpuonly==2.0 conda-forge::fsspec -c pytorch pip install pandas==1.4.3 matplotlib==3.8.2 networkx==3.1 argparse==1.4.0 scipy==1.11.4 scanpy==1.9.6 leidenalg==0.10.1 bambi==0.9.0 arviz==0.16.1 pyarrow numba==0.56.4 export MKL_THREADING_LAYER=GNU conda install numpy==1.22.0

The below file has the commands as shown above and the packages that resulted from that installation. scTIGER_PackageVersionsALL.txt

Please let me know if the dependency issue still appears on your end.

[utkarsh027]

Hi, I tried but this error is coming(attaching) , i followed every step .

On Mon, Apr 29, 2024 at 12:39 PM chenyongrowan @.***> wrote:

I see what happened. Pytorch released new versions and it is forcing certain packages to update which becomes incompatible with Bambi. I was just able to install scTIGER on my CPU processing machine with the following commands:

conda create -n scTIGER python=3.9.2 conda activate scTIGER conda install pytorch==2.1.2 torchvision==0.16.2 torchaudio==2.1.2 cpuonly==2.0 conda-forge::fsspec -c pytorch pip install pandas==1.4.3 matplotlib==3.8.2 networkx==3.1 argparse==1.4.0 scipy==1.11.4 scanpy==1.9.6 leidenalg==0.10.1 bambi==0.9.0 arviz==0.16.1 pyarrow numba==0.56.4 export MKL_THREADING_LAYER=GNU conda install numpy==1.22.0

The below file has the commands as shown above and the packages that resulted from that installation. scTIGER_PackageVersionsALL.txt https://github.com/chenyongrowan/scTIGER/files/15154025/scTIGER_PackageVersionsALL.txt

Please let me know if the dependency issue still appears on your end.

— Reply to this email directly, view it on GitHub https://github.com/chenyongrowan/scTIGER/issues/1#issuecomment-2083521536, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMQX3RTN62VMLMADJASQWATY72OWNAVCNFSM6AAAAABGYFZ2WGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBTGUZDCNJTGY . You are receiving this because you authored the thread.Message ID: @.***>

[chenyongrowan]

Can you please provide the error message you are seeing? I don't see anything attached to the last comment. It would be most helpful to have the commands and output you are getting from the command line. You can type "script" in the command line before running the above commands and it will provide a text file with this information that I can review.

[utkarsh027]

I have attached the screenshot in the last email. Also I will send You the script by today.

On Tue, Apr 30, 2024 at 5:34 AM chenyongrowan @.***> wrote:

Can you please provide the error message you are seeing? I don't see anything attached to the last comment. It would be most helpful to have the commands and output you are getting from the command line. You can type "script" in the command line before running the above commands and it will provide a text file with this information that I can review.

— Reply to this email directly, view it on GitHub https://github.com/chenyongrowan/scTIGER/issues/1#issuecomment-2085212457, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMQX3RUHQY6DCOWG3KNFFA3Y76FWNAVCNFSM6AAAAABGYFZ2WGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBVGIYTENBVG4 . You are receiving this because you authored the thread.Message ID: @.***>

[chenyongrowan]

I cannot see the screenshot in your reply on the thread. It may be that email attachments do not appear with the responses when replying via email. Can you please attach the screenshot and script to a response directly in the thread for documentation of the issue for others who may be experiencing a similar issue? Thank you!

[utkarsh027]

the error is this after following all steps-

(scTIGER) @.*** SCTIGER % cd SCTIGER

(scTIGER) @.*** SCTIGER % chmod +x run_scTIGER.py

(scTIGER) @.*** SCTIGER % unzip Data/ProstateCancer/Patient4_Benign_endothelial.zip -d ./Data/ProstateCancer/

Archive: Data/ProstateCancer/Patient4_Benign_endothelial.zip

inflating: ./Data/ProstateCancer/Patient4_Benign_endothelial.csv

(scTIGER) @.*** SCTIGER % ./run_scTIGER.py -goi AR+PTEN+ERG -ctrl ./Data/ProstateCancer/Patient4_Benign_endothelial.csv -exp ./Data/ProstateCancer/Patient4_Tumor_endothelial.csv -p 50 -top 100 -zero 0.15 -o SampleResult_ProstateCancer

Traceback (most recent call last):

File "/Users/utkarsh/scTIGER/scTIGER/./run_scTIGER.py", line 14, in

import scTIGER as sd File "/Users/utkarsh/scTIGER/scTIGER/scTIGER.py", line 12, in import bambi as bmb File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/bambi/__init__.py", line 3, in from pymc import math File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/pymc/__init__.py", line 52, in from pymc import gp, ode, sampling File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/pymc/gp/__init__.py", line 15, in from pymc.gp import cov, mean, util File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/pymc/gp/util.py", line 37, in from pymc.distributions.distribution import NoDistribution File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/pymc/distributions/__init__.py", line 21, in from pymc.distributions.bound import Bound File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/pymc/distributions/bound.py", line 23, in from pymc.distributions.continuous import BoundedContinuous, bounded_cont_transform File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/pymc/distributions/continuous.py", line 88, in from pymc.distributions.distribution import DIST_PARAMETER_TYPES, Continuous File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/pymc/distributions/distribution.py", line 50, in from pymc.printing import str_for_dist, str_for_symbolic_dist File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/pymc/printing.py", line 25, in from pymc.model import Model File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/pymc/model.py", line 64, in from pymc.initial_point import make_initial_point_fn File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/pymc/initial_point.py", line 28, in from pymc.util import get_transformed_name, get_untransformed_name, is_transformed_name File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/pymc/util.py", line 19, in import arviz File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/arviz/__init__.py", line 33, in from .data import * File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/arviz/data/__init__.py", line 2, in from .base import CoordSpec, DimSpec, dict_to_dataset, numpy_to_data_array File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/arviz/data/base.py", line 11, in import xarray as xr File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/xarray/__init__.py", line 3, in from xarray import testing, tutorial File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/xarray/testing.py", line 11, in from xarray.core.coordinates import Coordinates File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/xarray/core/coordinates.py", line 16, in from xarray.core.alignment import Aligner File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/xarray/core/alignment.py", line 24, in from xarray.core.variable import Variable, as_compatible_data, calculate_dimensions File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/xarray/core/variable.py", line 48, in from xarray.namedarray.core import NamedArray File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/xarray/namedarray/core.py", line 24, in from xarray.namedarray._typing import ( File "/Users/Shared/anaconda3/envs/scTIGER/lib/python3.9/site-packages/xarray/namedarray/_typing.py", line 28, in _DType = TypeVar("_DType", bound=np.dtype[Any]) TypeError: 'numpy._DTypeMeta' object is not subscriptable On Tue, Apr 30, 2024 at 10:38 AM chenyongrowan ***@***.***> wrote: > I cannot see the screenshot in your reply on the thread. It may be that > email attachments do not appear with the responses when replying via email. > Can you please attach the screenshot and script to a response directly in > the thread for documentation of the issue for others who may be > experiencing a similar issue? Thank you! > > — > Reply to this email directly, view it on GitHub > , > or unsubscribe > > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> >

[chenyongrowan]

Hi! Yes, that is a numpy issue. Can you try conda update numpy in your scTIGER environment?

I am currently working on setting up scTIGER as an Anaconda package, but may need a week or two to get everything set up correctly. Once that is complete, it should be much easier to download the package. Thanks for your patience as I work through this!

[utkarsh027]

When i am updating numpy it is showing compatibility issue with bambi. Let me know when you have resolved the error.

Thank you

On Sun, May 5, 2024 at 3:32 PM chenyongrowan @.***> wrote:

Hi! Yes, that is a numpy issue. Can you try conda update numpy in your scTIGER environment?

I am currently working on setting up scTIGER as an Anaconda package, but may need a week or two to get everything set up correctly. Once that is complete, it should be much easier to download the package. Thanks for your patience as I work through this!

— Reply to this email directly, view it on GitHub https://github.com/chenyongrowan/scTIGER/issues/1#issuecomment-2094975426, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMQX3RVBP75DA5PRZZJUWNLZA2XOLAVCNFSM6AAAAABGYFZ2WGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJUHE3TKNBSGY . You are receiving this because you authored the thread.Message ID: @.***>

[chenyongrowan]

I am not sure why it is giving a compatibility issue, I can't recreate the error on my end.

I have uploaded a very basic conda package to help set the package dependencies correctly. I updated our installation instructions to reflect this. I have not had a chance to test it on a CUDA capable machine yet, but it does work on CPU processing systems. I will test it on a CUDA capable machine later this week.

Can you try the following and let me know if you are able to successfully install?

conda create -n scTIGER 
conda activate scTIGER
conda install pytorch==2.1.2 torchvision torchaudio cpuonly==2.0 -c pytorch
conda install madison.dautle::sctiger

[utkarsh027]

I will do and let you know.

On Mon, May 6, 2024 at 11:25 PM chenyongrowan @.***> wrote:

I am not sure why it is giving a compatibility issue, I can't recreate the error on my end.

I have uploaded a very basic conda package to help set the package dependencies correctly. I updated our installation instructions to reflect this. I have not had a chance to test it on a CUDA capable machine yet, but it does work on CPU processing systems. I will test it on a CUDA capable machine later this week.

Can you try the following and let me know if you are able to successfully install?

conda create -n scTIGER conda activate scTIGER conda install pytorch==2.1.2 torchvision torchaudio cpuonly==2.0 -c pytorch conda install madison.dautle::sctiger

— Reply to this email directly, view it on GitHub https://github.com/chenyongrowan/scTIGER/issues/1#issuecomment-2097539451, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMQX3RVQRLLUF4IS4X56D2TZBBXVTAVCNFSM6AAAAABGYFZ2WGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJXGUZTSNBVGE . You are receiving this because you authored the thread.Message ID: @.***>

[chenyongrowan]

Hi! Due to the new package installation instructions and list of package dependencies from our operational installation of the package, we are going to resolve this issue. We hope you were able to install scTIGER!