hermie: the spectrum-to-protein analysis pipeline

Index

Below is a listing of all the topics covered on the various pages of the hermie documentation.

Before you begin	Perform one-time set-up steps, confirm that you have necessary accounts, files, etc.
An Example Run	Step-by-step walk through of an analysis using hermie
Using MS2 files from different locations	Three ways of specifying which MS2 files will be analyzed.
Running longer analyses	Tips for managing long runs including the use of nohup.
Checking on your run's progress	Four ways to confirm that the run is proceeding correctly.
Custom Search Modes	How to modify your run including how to change databases for the SEQUEST search.
Custom sequest.params	How to use a non-standard sequest.params file to, for example, search for modifications. This is not how to specify the database.
Understanding $MODEPATH	An explanation of the environment variable associated with the mode. Use this to get your custom mode working.
Example commands: full automation	Several examples of how to run hermie with the minimum input
Example commands: named output	Examples in which the output directory is named something other than 'pipeline'
Example commands: specify MS2 files	Two different ways to specify which MS2 files are analyzed
Example commands: custom database	Specify on the command line the use of your own database for the SEQUEST search.
Example commands: skipping steps	Each of the steps in the pipeline can be skipped.
Example commands: program options	Each step in the pipeline can have user-specified options passed to it.
Example commands: custom search modes	A brief review of how to use a custom search mode file.
Example commands: copy to web	An example of having the results file, DTASelect.html copied to a directory where it can be viewed from a web browser
Example commands: email notification	An example of how to receive an email message when your run has ended.
Example commands: crux	An example of how to run crux in addition to or instead of SEQUEST.