Error when install CellO

[Chrisdoan9]

Hello all,
I run:

pip install pygraphviz leidenalg scanpy cello-classify

And this was what I got:

 pygraphviz/graphviz_wrap.c:2711:10: fatal error: 'graphviz/cgraph.h' file not found
  #include "graphviz/cgraph.h"
           ^~~~~~~~~~~~~~~~~~~
  1 error generated.
  error: command '/usr/bin/clang' failed with exit code 1
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> pygraphviz

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

[notice] A new release of pip available: 22.2.2 -> 22.3
[notice] To update, run: python3.9 -m pip install --upgrade pip
(cello_env)

Would you please suggest how to fix this? Thank you so much!

[mbernste]

Hi, it looks like this is an issue with your graphviz installation. Do you know how you installed graphviz? I would recommend using conda:

conda install -c anaconda graphviz

[Chrisdoan9]

Thank you!

conda install -c anaconda graphviz returned no error, however:

pip install pygraphviz leidenalg scanpy cello-classify

#include "graphviz/cgraph.h"
^
compilation terminated.
error: command '/usr/lib64/ccache/gcc' failed with exit code 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> pygraphviz

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

[mbernste]

Sorry to hear you are still having trouble. You may want to try installing pygraphviz through conda as well: https://anaconda.org/conda-forge/pygraphviz

[Chrisdoan9]

Thank you! It worked!

model_prefix = 'GSM3516673_MSK_LX682_NORMAL′

File "", line 1
model_prefix = 'GSM3516673_MSK_LX682_NORMAL′
^
SyntaxError: EOL while scanning string literal

Would you please tell me how to fix this? Should I open a new issue or I can post the error here? Thank you.

[Chrisdoan9]

Hi,

I installed cello on a server, so it is different from a local computer when open Jupiter notebook. When I copied and pasted the URL as the instruction, I could not open Jupiter notebook. Would you please have a suggestion? Or I should install Cello on a local computer? Thank you so much!

(cello_env) [user@fenn03 ~]$ jupyter notebook cello_tutorial.ipynb
[I 14:02:24.637 NotebookApp] Serving notebooks from local directory: /home/user
[I 14:02:24.637 NotebookApp] Jupyter Notebook 6.5.1 is running at:
[I 14:02:24.637 NotebookApp] http://localhost:8888/?token=57c5937d21cc7ab01ceb08b66ba0a6bbfa45c7625175802d
[I 14:02:24.637 NotebookApp] or http://127.0.0.1:8888/?token=57c5937d21cc7ab01ceb08b66ba0a6bbfa45c7625175802d
[I 14:02:24.637 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[W 14:02:24.650 NotebookApp] No web browser found: could not locate runnable browser.
[C 14:02:24.650 NotebookApp]

To access the notebook, open this file in a browser:
    file:///home/user/.local/share/jupyter/runtime/nbserver-30005-open.html
Or copy and paste one of these URLs:
    http://localhost:8888/?token=57c5937d21cc7ab01ceb08b66ba0a6bbfa45c7625175802d
 or http://127.0.0.1:8888/?token=57c5937d21cc7ab01ceb08b66ba0a6bbfa45c7625175802d

[mbernste]

Hi Chris, Here's an article that may help you running a Jupyter notebook on a remote server using SSH tuneling: https://docs.anaconda.com/anaconda/user-guide/tasks/remote-jupyter-notebook/

[Chrisdoan9]

Thank you! It worked!

model_prefix = 'GSM3516673_MSK_LX682_NORMAL′

File "", line 1 model_prefix = 'GSM3516673_MSK_LX682_NORMAL′ ^ SyntaxError: EOL while scanning string literal

Would you please tell me how to fix this? Should I open a new issue or I can post the error here? Thank you.

Thank you for the information! Do you have any suggestions for this issue?

[cndewey]

It looks like your end quote character is not a standard Python quote character. Use ' instead of ′

[Chrisdoan9]

Thank you so much! I copied code from the paper and didn't check it.

[Chrisdoan9]

Hi,

Would you please have a look at this?

cello.scanpy_cello(

adata,

clust_key='leiden',

rsrc_loc=cello_resource_loc,

out_prefix=model_prefix,

log_dir=os.getcwd()

)

    Could not find the CellO resources directory called
    'resources' in '/vcu_gpfs2/home/doanc2'. Will download resources to current 
    directory.

Running command: curl http://deweylab.biostat.wisc.edu/cell_type_classification/resources_v2.0.0.tar.gz > /home/user/resources_v2.0.0.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 266 100 266 0 0 3782 0 --:--:-- --:--:-- --:--:-- 3855
Running command: tar -C /home/user -zxf resources_v2.0.0.tar.gz

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now
Running command: rm /vcu_gpfs2/home/doanc2/resources_v2.0.0.tar.gz
Checking if any pre-trained model is compatible with this input dataset...
Traceback (most recent call last):
File "", line 1, in
File "/home/user/miniconda3/envs/cello_env/lib/python3.7/site-packages/cello/scanpy_cello.py", line 129, in cello
mod = ce._retrieve_pretrained_model(adata, algo, rsrc_loc)
File "/home/user/miniconda3/envs/cello_env/lib/python3.7/site-packages/cello/cello.py", line 331, in _retrieve_pretrained_model
with open(model_f, 'rb') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/home/user/resources/trained_models/ir.dill'

[Chrisdoan9]

Hi,

Just check-in in case you weren't notified.