Update README.md

README.md

@@ -36,7 +36,9 @@ Follow the installation instructions [here](https://www.tensorflow.org/install).
 ## Usage
 1. Create a directory for the group of experiments. For example, `/media/big-ssd/experiments`. This is called the experiment base directory. All the intermediate artefacts and results produced by the pipeline will be stored in subdirectories created automatically under this directory.  
 2. Under the experiment base directory, create a directory for each experiment. For example, `P3856_YHE010` for the human-only data.  
-The pipeline expects the raw `.d` directories to be in a directory called `raw-databases` under the experiment directoy. Either copy the `.d` directories here, or save storage by creating symlinks to them. For example, the .d directories have been downloaded to `/media/timstof-output`, the symlinks can be created like this:  
+3. The pipeline expects the raw `.d` directories to be in a directory called `raw-databases` under the experiment directoy. Either copy the `.d` directories here, or save storage by creating symlinks to them. For example, the .d directories have been downloaded to `/media/timstof-output`, the symlinks can be created like this:  
     1. `cd /media/big-ssd/experiments/P3856_YHE010/raw-databases`
     2. `ln -s /media/timstof-output/* .`
-3. Edit the `./tfde/pipeline/bulk-run.sh` bash script to process the groups of technical replicates of the experiment. These are the runs that will be used to build the peptide library and from which the library peptides will be extracted. Be sure to specify the experiment base directory with the `-eb` flag, which has the value `/media/big-ssd/experiments` by default.  
+4. Edit the `./tfde/pipeline/bulk-run.sh` bash script to process the groups of technical replicates of the experiment. These are the runs that will be used to build the peptide library and from which the library peptides will be extracted. Be sure to specify the experiment base directory with the `-eb` flag, which has the value `/media/big-ssd/experiments` by default.  
+5. Execute the pipeline with `./tfde/pipeline/bulk-run.sh`. Progress information is printed to stdout. Analysis will take a number of hours, depending on the complexity of the samples, the length of the LC gradient, and the computing resources of the machine. It's convenient to use a command like this for long-running processes: `nohup ./tfde/pipeline/bulk-run.sh > tfde.log 2>&1 &`.
+