Problem when installing MAJIQ/Voila

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Dario Dattilo

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Jul 18, 2023, 10:53:59 AM7/18/23
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Hi everyone,
I've recently installed majiq/voila in a conda env, following the academic download page guidelines.

When installing through pip I get the following output:

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.

jupyterlab-server 2.23.0 requires jinja2>=3.0.3, but you have jinja2 2.11.1 which is incompatible.

nbconvert 7.6.0 requires jinja2>=3.0, but you have jinja2 2.11.1 which is incompatible.

nbconvert 7.6.0 requires markupsafe>=2.0, but you have markupsafe 1.1.1 which is incompatible.

Successfully installed Click-7.1.2 Flask-1.1.4 Flask-Session-0.3.1 Flask-WTF-0.14.2 GitPython-3.0.5 Jinja2-2.11.1 MarkupSafe-1.1.1 WTForms-2.2.1 Werkzeug-0.16.0 decorator-5.1.1 gitdb2-2.0.6 gunicorn-19.9.0 h5py-3.7.0 itsdangerous-1.1.0 networkx-2.5 psutil-5.6.7 rna-majiq-2.4.dev102+g2cae1507 rna-majiq-meta-2.4.dev102+g2cae1507 rna-voila-2.4.dev102+g2cae1507 six-1.14.0 smmap2-2.0.5 waitress-1.1.0


Is this incompatibility normal?

Moreover, when I run majiq through a snakemake workflow I get the following error during my pipeline:


    from jinja2 import escape
ImportError: cannot import name 'escape' from 'jinja2'


This error seems to be dependant on the installed version of jinja2, but if I try to upgrade it I then end up with new conflicts.


Do you know if this issue is normal?


Thank you in advance.


Kind regards,

Dario Dattilo

San Jewell

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Aug 9, 2023, 6:26:32 PM8/9/23
to Biociphers
Hi Dario,

The official method uses python virtual environments rather than conda for installation, though I know many have had success with conda as well.

Can you show the exact commands you are using to create and install to the environment? Also which version of python are you requesting with conda environment creation? It should be 3.10 at this time.

Let me know when you have a chance,
-San
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