From d2242ee102305528328cac11b1cc97c933c5ed63 Mon Sep 17 00:00:00 2001 From: patrick_flege <patrick.flege@wur.nl> Date: Thu, 19 Dec 2024 16:20:10 +0100 Subject: [PATCH] Updated snakemake version explicitly --- docs/source/getting_started/diy_pangenomics.rst | 2 +- docs/source/tutorial/tutorial_part4.rst | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source/getting_started/diy_pangenomics.rst b/docs/source/getting_started/diy_pangenomics.rst index 7017a90a7..89dba3ba9 100644 --- a/docs/source/getting_started/diy_pangenomics.rst +++ b/docs/source/getting_started/diy_pangenomics.rst @@ -49,7 +49,7 @@ cause issues for tools like PanTools). This pipeline can be found at https://github.com/PanUtils/pantools-qc-pipeline which includes a README on how to install and run it. In summary, one needs to create a conda environment with the most recent version of Snakemake (at the moment of writing this is -7.32.4). Please follow the instructions on which configuration to set and +8.25.5). Please follow the instructions on which configuration to set and where all files should be placed. The pipeline has four different workflows: diff --git a/docs/source/tutorial/tutorial_part4.rst b/docs/source/tutorial/tutorial_part4.rst index a55e975d9..49ecd3490 100644 --- a/docs/source/tutorial/tutorial_part4.rst +++ b/docs/source/tutorial/tutorial_part4.rst @@ -126,7 +126,7 @@ versions <= 3.11). .. code:: bash - $ mamba create -c conda-forge -c bioconda -n snakemake snakemake + $ mamba create -c conda-forge -c bioconda -n snakemake snakemake=8 If you are using an ARM-based machine (such as an M4-based Mac), make sure to make the new environment compatible with Intel-based packages. @@ -143,7 +143,7 @@ Please use this command to set up your environment: .. code:: bash - $ CONDA_SUBDIR=osx-64 mamba create -c conda-forge -c bioconda -n snakemake snakemake + $ CONDA_SUBDIR=osx-64 mamba create -c conda-forge -c bioconda -n snakemake snakemake=8 This command ensures that packages are downloaded for an Intel architecture. Afterwards, restart your shell with the "Open using Rosetta"-setting enabled. -- GitLab