Update documentation

docs/concepts.rst

@@ -53,13 +53,11 @@ repository can contain the following elements:
 * 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.
+be set by defining the environment variable `PSOT_REPOSITORIES` with a ':'
+separated list of paths.
 
 The repositories are loaded in the following order. Later respositories 
 overwrite values from previous repositories.
 
 * default repository
 * PSOT_REPOSITORIES
-* `-r` repositories

docs/index.rst

@@ -12,8 +12,10 @@ Welcome to PSOT - protein sequence observation tool's documentation!
 
    concepts
    installation
+   usage.rst
    modules
    profiles
+   repositories
 
 
 Indices and tables

docs/installation.rst

@@ -28,14 +28,32 @@ Installation
 ------------
 
 Install nextflow::
-    
+
     curl -fsSL get.nextflow.io | bash 
 
+(Optional) create a virtual env::
+
+    virtualenv --python=python3 venv
+    source venv/bin/activate
+
+Install dbxref and psot::
+
+    pip3 install git+https://git.computational.bio.uni-giessen.de/SOaAS/dbxref.git
+    pip3 install git+https://git.computational.bio.uni-giessen.de/SOaAS/psot.git
+
+Install a default repository for your profiles and modules::
+
+    TODO
+
+Developer setup
+---------------
+
 Clone the git repository of PSOT::
 
     git clone git@git.computational.bio.uni-giessen.de:SOaAS/psot.git
 
-Configuration
--------------
+Install it into a virtualenv::
 
-Adapt the paths in the config.yaml to your needs.
+    virtualenv --python=python3 venv; source venv/bin/activate;
+    pip3 install git+https://git.computational.bio.uni-giessen.de/SOaAS/dbxref.git
+    pip3 install -e .

docs/modules.rst

@@ -5,7 +5,7 @@ Modules
 
 A module specifies exactly one analysis that can be run within PSOT. Each
 module has a default configuration that is specified in its manifest. During the
-execution a module will run through two phases: the analysis and the conversion
+execution, a module will run through two phases: the analysis and the conversion
 phase. The phases are implemented as commandline tools that have at least the
 following parameters:
 
@@ -19,6 +19,10 @@ following parameters:
   * ``--result`` - the result from the analysis step
   * ``--output`` - the converted json file
 
+The scripts can have additional parameters. They can be set in the paramaters
+section of the module manifest. The parameters can be overridden in the
+profile.
+
 A module manifest has the following structure::
 
     # Module manifest for the blastp against swissprot analysis
@@ -45,5 +49,4 @@ A module manifest has the following structure::
 	parameters:
 	    dbxref: UniProtKB/Swiss-Prot
 
-These parameters can be overridden in the profile.
 

docs/repositories.rst

+Structure of a repository
+=========================
+
+A repository contains one or multiple modules and profiles. It defines a
+directory structure. 
+
+A repository has the following structure::
+    ./repository/
+                 config.yaml
+                 profiles/
+                          profile1.yaml
+                          profile2.yaml
+                 modules/
+                         module1.yaml
+                         module2.yaml
+                 scripts/
+                         run_tool1.yaml
+                         run_tool2.yaml
+                         convert_tool1.yaml
+                         convert_tool2.yaml
+
+
+You can include your own repository by setting the PSOT_REPOSITORIES
+environment variable.

docs/usage.rst

+PSOT usage
+==========
+
+PSOT comes along as the commandline tool `psot`. It has two subcommands::
+
+  info    -> show information about available modules and profiles
+  analyze -> runs a profile for a protein fasta file
+
+
+Basic execution
+---------------
+
+::
+
+  psot analyze -f myfasta.faa -o results -p fast
+
+
+Live mode execution
+-------------------
+
+During live mode execution PSOT will output results for already finished
+modules as soon they become ready into a subfolder `live` within the results
+folder.
+
+::
+
+  psot analyze -f myfasta.faa -o results -p fast -l
+
+Cluster mode
+------------
+
+PSOT can take leverage of your compute cluster. At the moment it only supports
+SGE. To use the cluster set the `-C` option.
+
+::
+
+  psot analyze -f myfasta.faa -o results -p fast -l -C
+
+Debug mode execution
+--------------------
+
+PSOT has a few options for debugging. You can specify the execution directory
+for the generated nextflow script via `-e <path>` and output the configuration
+state via `-d`. If `-e` and `-d` are both specified then the execution
+directory will not be removed.
+
+::
+  
+  psot analyze -f myfasta.faa -o results -p fast -l -C -e ~/my_exec_dir -d