push the first beta version 0.1

VERSION

-0.1.0a1
\ No newline at end of file
+0.1.0b1
\ No newline at end of file

doc/sphinx/source/index.rst

@@ -9,9 +9,9 @@ Org.Asm: |Orgasm|
 Contents:
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
 
-   install 
+   install
    strategies
    oa
    mitochondrion

doc/sphinx/source/install.rst

@@ -119,4 +119,4 @@ From the directory where you retrieved the sources, execute the following comman
       > python3 setup.py --serenity install
 
 Once installed, you can test your installation by running the commands of the
-:doc:`tutorials <./tutorials>`.
+:doc:`tutorials <./mitochondrion>`.

doc/sphinx/source/mitochondrion.rst

@@ -446,11 +446,13 @@ prefix indicated as second parametter.
     tools accepting the Graph Modeling Language (`GML`_) format. For this
     purpose we are usualy using the `Yed <yed>`_ program.
 
-    The ``butterfly.mito.intermediate.gml`` file is produced regularly during
-    the assembling process by the :ref:`oa index <oa_index>` command. It gives
-    oportunity for following the assembling process during its computation.
+    The :download:`butterfly.mito.intermediate.gml <../../../samples/butterfly.mito.intermediate.gml>`
+    file is produced regularly during the assembling process by the
+    :ref:`oa index <oa_index>` command. It gives opportunity for following
+    the assembling process during its computation.
 
-    The ``butterfly.mito.gml`` contains the final assembling graph.
+    The :download:`butterfly.mito.gml <../../../samples/butterfly.mito.gml>`
+    contains the final assembling graph.
 
     These files are produced for the user convinience and they are not
     reuse latter by the assembler.
@@ -533,6 +535,12 @@ relationship.
     Compacting graph 100.0 % |#################################################\ ] remain : 00:00:00
     Minimum stem coverage = 393
 
+On such assembling graph each contig can be assimilated to a path linking a
+subset of vertices of a connected componante. Exploring connecting componante
+can by expensive in computation time. To increase our change to find a solution
+a heuristic is applyed on the graph to identify the connected componantes that
+have a good chance to correspond to the targeted genome.
+
 .. code-block:: bash
 
     2015-08-17 12:25:19,786 [INFO ]  Select the good connected componantes
@@ -541,16 +549,27 @@ relationship.
     Coverage 1x = 396
     Path is circular
 
+The selected componante(s) is/are analyzed to find an optimal path in them
+and the corresponding sequence is printed out in a fasta file. If you look at
+the file now contained by the current folder
 
 .. code-block:: bash
 
     ls -l
 
+You can observe two new files.
+
 .. code-block:: bash
 
     -rw-r--r--  1 coissac  staff    31087 17 aoû 12:25 butterfly.mito.fasta
     -rw-r--r--  1 coissac  staff   252144 17 aoû 12:25 butterfly.mito.path.gml
 
+
+The  :download:`butterfly.mito.path.gml <../../../samples/butterfly.mito.path.gml>`
+file contains a simplified graph representation of the assembling similar to the
+one produced by the :ref:`oa buildgraph <oa_buildgraph>` command but including
+moreover information about the selected path.
+
 .. figure:: butterfly.mito.path.*
   :align: center
   :figwidth: 80 %
@@ -561,7 +580,11 @@ relationship.
   It can be visualized using the `Yed <yed>`_ program
 
 
-butterfly.mito.path
+The :download:`butterfly.mito.fasta <../../../samples/butterfly.mito.fasta>`
+file contains the produced sequence in fasta format. Most of the time you have
+a single contig corresponding to the complete sequence of the targeted genome.
+You can read this file using your favorite sequence/text editor or using the
+**Unix** ``cat`` command.
 
 .. code-block:: bash
 

doc/sphinx/source/oa.rst

@@ -3,6 +3,10 @@
 The ORGanelle ASseMbler command line
 ====================================
 
+|Orgasm| is run using the :ref:`oa <oa>` Unix command. It is providing
+a set of sub-commands allowing for the complete assembling of small genomes
+(organelle genomes) from a genome skimming sequence dataset. You can have a
+basic idea on how to proced by following the :doc:`tutorial <./mitochondrion>`.
 
 The ORGanelle ASseMbler commands
 --------------------------------
@@ -12,7 +16,7 @@ The ORGanelle ASseMbler commands
   :figwidth: 80 %
   :width: 500
 
-  The :ref:`organelle assembler <oa>`'s proides a set of commands.
+  The :ref:`organelle assembler <oa>`'s provides a set of commands.
 
   Several of these commands (at least three) have to executed to complete
   an assembling process.
@@ -27,6 +31,9 @@ The ORGanelle ASseMbler commands
       assembling but sometime useful to get or restore some information.
 
 
+The set of sub-commands can be splitted in several categories corresponding to
+the main steps of the assembling procedure.
+
 .. toctree::
    :maxdepth: 2
 

python/orgasm/version.py

 major = 0
 minor = '1'
-serial= '0a0'
+serial= '0b1'
 
 version = "%2d.%s.%s" % (major,minor,serial)