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Enhance README with manual container binding instructions #31

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9 changes: 8 additions & 1 deletion README.md
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Expand Up @@ -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)
Expand Down Expand Up @@ -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

Expand Down