Conda install failure

[mpolemis]

Dear ReporTree Team,
I attempted to install ReporTree on a server running Ubuntu 20.04.6 LTS, following the instructions provided in your documentation. Unfortunately, the "pytest" failed.
Please find the full error report attached for your review.
errors_to_report.txt

I would appreciate any guidance you can provide to help resolve this issue.
Thank you in advance!
Michalis

[vmixao]

Hi @mpolemis

Thanks for your interest in ReporTree.

Can you please send us the exact list of commands you run from installation until pytest?

Also, can you please send us the outputs of the following command line:

which conda

and

conda env list | grep reportree

Thanks!!
Cheers
Veronica

[mpolemis]

Hi Veronica,
Just to clarify, the commands I used were directly copied and pasted from your instructions.

git clone https://github.com/insapathogenomics/ReporTree cd ReporTree/scripts git clone https://github.com/insapathogenomics/GrapeTree.git git clone https://github.com/insapathogenomics/ComparingPartitions.git git clone https://github.com/insapathogenomics/vcf2mst.git cd .. conda env create --name reportree --file=reportree_env.yml

history.txt

Cheers,
Michalis

[vmixao]

Hi,

Thanks!

But when you activated the environment were you using the same conda? I am asking because the only time we observed this error was when we tried to activate reportree environment using a conda different from the one where the environment was installed.

Can you please send us the outputs of the following command line:

which conda

and

conda env list | grep reportree

Cheers

[mpolemis]

Here are the outputs
which conda
/home/adminhera2/miniconda3/bin/conda

conda env list | grep reportree
reportree * /home/adminhera2/.conda/envs/reportree

Cheers

[vmixao]

It seems that the path of your conda and the path of the conda environment do not match. I would expect the environment to be in /home/adminhera2/miniconda3/envs/reportree.

Can you please remove the environment, repeat the installation and again check whether the environment is being saved in the right place?

[mpolemis]

I tried to create a new "test" environment (conda create --name test) and it was created at
test /home/adminhera2/.conda/envs/test

All conda envs on the server are at /home/adminhera2/.conda/envs/

[mpolemis]

I fixed the envs folder... it was a permissions issue.
Now
conda env list | grep reportree
reportree /home/adminhera2/miniconda3/envs/reportree

Unfortunately pytest gives the same errors...
:(

[vmixao]

Hi @mpolemis

Thanks for your feedback!

I am trying to figure out what is going on. As I said before, the only way I can reproduce the error is when I run the pytest with a conda that is different from the conda I used to install. When I ensure that my conda bin and my conda envs are in the same directory, everything works.

Can you please send me the pytest error you are getting now? I understand that the error is the same, but I want to check from where the program is now trying to import the python modules.

Thanks!

[vmixao]

Hi @mpolemis

Can you please send me the pytest error you are getting now, so I can try to help? I understand that the error is the same, but I want to check from where the program is now trying to import the python modules.

Cheers

[mpolemis]

Dear Veronica,
sorry for the delayed responce.

Here's the pytest output.
pytest_output.txt

Cheers,
Michalis

[vmixao]

Hi @mpolemis

Thank you!

I think that although you activate reportree environment, your system keeps using the python of your base:
../miniconda3/lib/python3.12/

If this is what's happening, this issue is related with some python/conda conflicts in your system. To check whether this is the case, can you please:

1. Open a new terminal
2. then run

which conda
which python 
conda activate reportree
which python

If the output of the last command is not the python of reportree environment, can you please:

1. Open a new terminal
2. then run

which conda
which python 
conda deactivate
which conda
which python
conda activate reportree
which python

Please paste your outputs here.

Thanks in advance!!!!

[mpolemis]

Here's the output

(base) :~$ which conda
/home/adminhera2/miniconda3/bin/conda
(base) :~$ which python
/home/adminhera2/miniconda3/bin/python
(base) :~$ conda activate reportree
(reportree) :~$ which python
/home/adminhera2/miniconda3/envs/reportree/bin/python

It seems that the python path is the correct one...

[vmixao]

Thanks!

I am sorry, this is taking me a while to understand what is going on. Can you please confirm that in this new terminal pytest still does not work? If you notice, the header of your previous pytest log says:

"platform linux -- Python 3.12.4, pytest-7.4.4, pluggy-1.0.0"

This means that the python your system was using before when you ran the command line was not the one of ReporTree installation (which is 3.8 and the one your which python command is showing you)...

If pytest is still not working, can you please open a new terminal and run:

which python
conda deactivate
which python
conda activate reportree
which python
python

2. Inside the python terminal please run:

import sys
print(sys.executable)

And send us a screenshot!

Also, can you please export your reportree environment to a yml file and send it to me?

conda env export > reportree_mpolemis.yml

Thanks!

[mpolemis]

Hi!!
Here's the output of pytest from the latest ReporTree environment..
pytest_output.txt

Here's the screenshot of the new terminal with the commands...

Here's the environment export file...
reportree_mpolemis.zip

Thank you for your effort in identifying the problem with our setup!
Cheers!
Michalis