From ededd634f553e952349b9088bc6968776e9e30c8 Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Mon, 3 Aug 2026 11:46:06 +0100 Subject: [PATCH] mamba -> conda, github -> pypi (for linux) This is a suggestion. The core dependency resolution work in mamba is now used by default in conda, so there is less reason to require the additional dependency on the mamba command line tool. You also now have formal releases on PyPI so installing from there is preferable for tracking a known version - and as a stepping stone to having this packaged in bioconda too. --- README.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) 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