From a3d7b6d4f5f35bd941f7a0c35e1766a8e53fe590 Mon Sep 17 00:00:00 2001 From: Anne Bertolini Date: Mon, 22 Jan 2024 14:38:53 +0100 Subject: [PATCH] [DOC] Adapt section about dsb and cellranger in README --- README.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 3e962bf..b782703 100644 --- a/README.md +++ b/README.md @@ -47,14 +47,13 @@ Note: Snakemake needs to access the internet for this set up. With Snakemake 7.1 ### Dependencies -Most of the software used in the default workflow can be installed in an automated fashion using Snakemake's [--use-conda](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#integrated-package-management) functionality when running the pipeline. -In case you would like to start from the raw sequencing data using cellranger processing, the following software needs to be installed manually. +Most of the software used in the default workflow can be installed in an automated fashion using Snakemake's [--use-conda](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#integrated-package-management) functionality when running the pipeline. Exceptions that must be downloaded or installed manually are listed below. + - [Cellranger](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger): Follow the instructions on the 10xGenomics installation support page to install cellranger and to include the cellranger binary to your path. Webpage: [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation) -The `dsb` CRAN package is not available on Conda. Therefore, a singularity image `dsb_r-base_4.2.3.sif` containg `dsb` and all other R packages necessary for this step is available for download at [here](https://depot.nexus.ethz.ch/software/multi_tool_container_stack/dsb_r-base_4.2.3.sif). -Please download the image and then provide the path in the config section "dsb_normalize_adt" -> "singularity". +- `dsb` CRAN package: is not available on Conda. Therefore, a singularity image `dsb_r-base_4.2.3.sif` containg `dsb` and all other R packages necessary for this step is available for download [here](https://depot.nexus.ethz.ch/software/multi_tool_container_stack/dsb_r-base_4.2.3.sif). Please download the image and then provide the path in the config section "dsb_normalize_adt" -> "singularity". ## Before running the pipeline