Skip to content

mamba -> conda, github -> pypi (for linux) #82

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
nextgenusfs merged 1 commit into from
Aug 3, 2026
Merged

mamba -> conda, github -> pypi (for linux) #82

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 5 additions & 4 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -63,11 +63,12 @@ The pixi environment is currently defined for `linux-64` only. macOS users shoul

#### Linux systems (conda)

Until this gets pushed to bioconda, can try this:
Until this gets pushed to bioconda, you can try this:

```shell
mamba create -n funannotate2 gfftk gapmm2 minimap2 miniprot snap "augustus==3.5.0" glimmerhmm diamond trnascan-se table2asn gb-io buscolite
conda create -n funannotate2 gfftk gapmm2 minimap2 miniprot snap "augustus==3.5.0" glimmerhmm diamond trnascan-se table2asn gb-io buscolite
conda activate funannotate2
python -m pip install git+https://github.com/nextgenusfs/funannotate2.git
python -m pip install funannotate2
```

#### Apple Silicon (M series)
Expand All @@ -81,7 +82,7 @@ Once that is working, you can then install most of the remaining dependencies wi

```shell
# first install most of the dependencies
mamba create -n funannotate2 --platform osx-64 "python>=3.7,<3.13" gfftk gapmm2 minimap2 miniprot snap glimmerhmm diamond trnascan-se gb-io pyhmmer pyfastx requests json-repair pytantan "mkl<2022"
conda create -n funannotate2 --platform osx-64 "python>=3.7,<3.13" gfftk gapmm2 minimap2 miniprot snap glimmerhmm diamond trnascan-se gb-io pyhmmer pyfastx requests json-repair pytantan "mkl<2022"

# we can then add the required FUNANNOTATE2_DB env variable to the conda environment, note need to reactivate to use it
conda activate funannotate2
Expand Down
Loading