To retrieve the transcript from gff file with the longest isoform

Question

[Aneesha]

When I installed AGAT using conda environment in ubuntu, I got a conflict as,

Package libgcc-ng conflicts for:

agat -> libdb -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.3.0']
python=3.8 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0']
python=3.8 -> libgcc-ng[version='>=7.3.0|>=7.5.0']

How can I rectify this? Even after I updating conda, anaconda, python3.8 and r base.

Thank you

[Lila M]

Have a look into this post , it may help.

[i.sudbery]

This post's content does seem to match the title, can you please pick a more appropriate title, more connected to the installation difficulties you are having.

[Juke34]

You probably had some other tools installed in the environnement you are using that have dependencies conflicts. The rule of thumb you should follow with conda is to use as most as possible one tool by environment.

So create a dedicated environment for agat should fix your problem:

# create an environment called agat
conda create -n agat
# move into the environement called agat
conda activate agat
# install the tool called agat
conda --install -c bioconda agat

[Aneesha]

It's working, I installed successfully and got required results.

Thank you, Aneesha

[Aneesha]

Thank you all for your valuable inputs.