diff --git a/README.md b/README.md index 380f6db..338fbbf 100755 --- a/README.md +++ b/README.md @@ -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) @@ -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