Fixed version an updated install docs

ChangeLog

@@ -1,7 +1,11 @@
-Version 0.36.2
+Version 0.37.0
+  * Warn or error when bowtie2 versions that give inconsistent or problematic
+    output are used. Update conda recipe to install the recommended bowtie2
+    version 2.2.4 to try to enforce consistency.
+  * Added back code for shifting indels to improve mutation calling.
   * Added an option for gdtools APPLY to output a new GD file showing the
     positions of each mutation in the (mutated) output genome.
-  * Improved documentation related to explaining junction orientations.
+  * Updated documentation related to installation and explaining junction orientations.
   * Fixed crash that could occur if there was a deletion spanning the origin of a
     circular reference sequence.
 

configure.ac

@@ -19,7 +19,7 @@
 #                                               -*- Autoconf -*-
 # Process this file with autoconf to produce a configure script.
 AC_PREREQ([2.65])
-AC_INIT([breseq], [0.36.2], [[email protected]], [breseq], [http://barricklab.org/breseq])
+AC_INIT([breseq], [0.37.0], [[email protected]], [breseq], [http://barricklab.org/breseq])
 AC_CONFIG_AUX_DIR(aux_build)
 AC_CONFIG_MACRO_DIR([aux_build/m4])
 AC_CONFIG_HEADERS([aux_build/config.h])

src/doc/installation.rst

@@ -1,25 +1,37 @@
 Installation
 ==============
 
-|breseq| is a command line tool implemented in C++ and R. It is compatible with a variety of UNIX-like platforms, including Linux, MacOSX, and Windows Subsystem for Linux (WSL).
+|breseq| is a command line tool implemented in C++ and R. It is compatible with a variety of UNIX-like platforms, including Linux, MacOSX, and Windows Subsystem for Linux (WSL). There are several ways to install it described below.
 
-The most recent |breseq| binary distributions and source code packages are available for download from `GitHub <https://github.com/barricklab/breseq/releases>`_.
-The instructions in the following sections explain how to install |breseq| using these files.
+If you are not comfortable with running commands in a terminal, it is also possible to install and use |breseq| on the web-based `Galaxy platform <https://usegalaxy.org>`_ (See `Installing on Galaxy`_).
+
+Recommended Method: Install |breseq| using Conda
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
 .. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
    :target: http://bioconda.github.io/recipes/breseq/README.html
 
-**New:** Another installation option is to use the `Conda package manager <https://docs.conda.io/en/latest/>`_ to install |breseq| and all of the programs it requires. Make sure you have
+The recommended installation method is to use the `Conda package manager <https://docs.conda.io/en/latest/>`_ to install |breseq| and all of the programs it requires. Make sure you have
 `Bioconda <https://bioconda.github.io/user/install.html>`_ set up, then follow the directions for the `breseq package <http://bioconda.github.io/recipes/breseq/README.html>`_.
 
+.. NOTE::
+   If you get an install error about the |Bowtie2| requirement not being satisfied, you need to create a Conda environment that uses Python 3.9 or earlier. These commands will do that and install |breseq|.
 
-.. image:: images/galaxy.png
-   :target: https://usegalaxy.org
+   .. code-block:: bash
 
-**New:** If you are not comfortable with running commands in a terminal, it is also possible to install and use |breseq| on the web-based `Galaxy platform <https://usegalaxy.org>`_ (See `Installing on Galaxy`_).
+      $ conda create -n breseq python=3.9
+      $ conda activate breseq
+      $ conda install breseq
+
+
+Normal Method: Install |breseq| on your own
++++++++++++++++++++++++++++++++++++++++++++++
+
+The most recent |breseq| binary distributions and source code packages are available for download from `GitHub <https://github.com/barricklab/breseq/releases>`_.
+The instructions in the following sections explain how to first install the programs |breseq| needs to run and then |breseq| itself. You can use any of the three options shown for installing |breseq| executables.
 
 Install external dependencies
-++++++++++++++++++++++++++++++
+-------------------------------------
 
 |breseq| requires these software programs to be installed on your system:
 
@@ -33,8 +45,9 @@ To install each dependency, visit the respective web pages linked above and foll
 
    Output of |breseq| may vary slightly depending on your version of |Bowtie2|. When reporting |breseq| results in a publication you should always report the version of |breseq| you used and also the version of |Bowtie2|. Currently, we recommend using |Bowtie2| version 2.4.4. This is the version used by the consistency tests.
 
+
 Method 1. Binary download
-+++++++++++++++++++++++++++++
+-------------------------------------
 
 Linux and MacOSX packages with precompiled executables are available for download. Using these is the quickest and easiest install option that should be used by most users.
 
@@ -58,7 +71,7 @@ You may also run this command to test the |breseq| install:
 .. _installing-source-code-package:
 
 Method 2. Source code download
-++++++++++++++++++++++++++++++
+-------------------------------------
 
 |breseq| installation from the source code requires some basic familiarity with UNIX commands and environments.
 
@@ -143,19 +156,22 @@ For a :program:`bash` shell you can usually use a command like this:
 But the exact way to do this may depend on your system. You may also want to similarly update your $MANPATH, $CPPFLAGS, $LD_FLAGS, etc. Now you should be able to invoke |breseq| commands once you open a new terminal window.
 
 Method 3. GitHub source code
-+++++++++++++++++++++++++++++++++
+-------------------------------------
 
 If you are working with a development version of |breseq| cloned from the `GitHub code repository <https://github.com/barricklab/breseq>`_, then you will need to run some additional commands and have other tools installed on your system in order to get it to compile or work with the XCode project.
 
 These requirements and commands are detailed in the DEVELOPER text file located in the main directory of the source code.
 
 Installing on Windows (using WSL)
-+++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++
 
 Download and install `Windows Subsystem for Linux (WSL) <https://docs.microsoft.com/en-us/windows/wsl/about>`_ on your machine. In the WSL terminal, you should be able to use any of the methods described above for installation. For example, you can install Conda and then use it to install the |breseq|.
 
 Installing on Galaxy
-+++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++
+
+.. image:: images/galaxy.png
+   :target: https://usegalaxy.org
 
 If you administer a Galaxy server, |breseq| is available to install from the `Main Tool Shed <https://toolshed.g2.bx.psu.edu/>`_. See also, the directions for `Installing Tools into Galaxy <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`_.