From 30af80dba9da98a46ca9574db8327f8b1cef857a Mon Sep 17 00:00:00 2001 From: Thomas Bradley Date: Tue, 27 Jan 2026 15:47:58 +0000 Subject: [PATCH] Enhance README with manual container binding instructions Added instructions for manually binding current working directory to container and clarified error resolution steps. --- README.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index f0709a6..6a31bce 100644 --- a/README.md +++ b/README.md @@ -82,6 +82,10 @@ snakemake --cores 16 --snakefile workflow/Snakefile_absolute \ --singularity-args "-B /home/${USER}/.cache -B /home/${USER}/scAbsolute:/opt/scAbsolute" ``` +This command should automatically bind your current working directory into the container's current working directory so that the container has access to +this repository's code and data which it needs run scAbsolute. If errors are generated related to lacking access to needed code or scripts this problem +could be resolved by appending ` -B ${PWD}:${PWD}` to `--singularity-args` in the above command. + ### QC analysis Please take the time to analyze the data (the qc script to be used for this step is available at scripts/qc-script.R) @@ -110,7 +114,10 @@ snakemake --cores 16 --snakefile workflow/Snakefile_unique \ --singularity-args "-B /home/${USER}/.cache -B /home/${USER}/scUnique:/opt/scUnique -B /home/${USER}/scAbsolute:/opt/scAbsolute" ``` -Results are then available in results/sample_name. +Results are then available in results/sample_name. + +Similarly to guidance on use of the scAbsolute container above, incorrect workspace binding into the container can be solved by appending ` -B ${PWD}:${PWD}` into +`--singularity-args` ### More examples and explanations