Update documentation

docs/concepts.rst

@@ -11,17 +11,20 @@ Vocabulary
 ----------
 
 Module
-    A module implements a bioinformatic tool and the corresponding json converter.
-    It is defined in a module manifest.
+    A module implements a bioinformatic tool and the corresponding json
+    converter.  It is defined in a module manifest.
 
 Profile
-    A profile is a set of modules that are executed during an execution of PSOT.
-    Profiles can override default parameters of modules.
+    A profile is a set of modules that are executed during an execution of
+    PSOT.  Profiles can override default parameters of modules.
+
+Repository
+    A collection of profiles, modules, scripts and configurations.
 
 Workflow
 --------
 
-1. Load all module manifests and profiles
+1. Load all module manifests and profiles from all available repositories
 2. Create an execution directory
 3. Generate a nextflow script for the choosen profile in the execution directory
 4. Run the nextflow script
@@ -33,6 +36,30 @@ Structure of the Nextflow Script
 1. Run all analyses in parallel
 2. Convert all analyses in parallel
 3. In live mode: generate a json document for each module and each sequence within the live directory
-4. Join all json files into a single one containing all information
-5. Split the large json file into separate files for each sequence
+4. In retrieve mode: retrieve all information from the referenced databases
+5. Join all json files into a single one containing all information
+6. Split the large json file into separate files for each sequence
+
+
+Loading of configuration artifacts
+----------------------------------
+
+Profiles, modules and configurations are organized in repositories. A
+repository can contain the following elements:
+
+* config.yaml (file)
+* modules/ (directory with yaml files)
+* profiles/ (directory with yaml files)
+* scripts/ (directory with scripts for modules)
+
+PSOT uses a repository search path to find bundled and own repositories. It can
+be either set by defining the environment variable `PSOT_REPOSITORIES` with a
+':' separated list of paths or by passing the repositories via one or multiple
+`-r` arguments.
+
+The repositories are loaded in the following order. Later respositories 
+overwrite values from previous repositories.
 
+* default repository
+* PSOT_REPOSITORIES
+* `-r` repositories

docs/index.rst

@@ -13,6 +13,7 @@ Welcome to PSOT - protein sequence observation tool's documentation!
    concepts
    installation
    modules
+   profiles
 
 
 Indices and tables

docs/installation.rst

@@ -9,6 +9,7 @@ In order to run PSOT on your machine you need:
 * git
 * python >= 3
 * nextflow
+* dbxref library
 * the bioinformatic tools you want to use
 
   * blastp

docs/profiles.rst

+.. highlight:: yaml
+
+Profiles
+========
+
+A profile specifies a set of analysis (modules) that can be run within PSOT.
+Each profile consists of a list of modules and corresponding configuration overrides.
+
+A profile manifest has the following structure::
+
+	# The name of the profile
+	name: 'fast'
+	
+	# Short description of the profile
+	info: 'Profile that contains tools that give a fast result'
+	
+	# A list of modules that belong to the profile. They must exist in the same
+	# repository.
+	modules:
+	  ghostx_swissprot:
+	  signalp:
+		  # configuration override for the module
+		  organism: 'euk'
+	  tmhmm:
+
+You can integrate your own profiles into psot by adding your own repositories.