--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Wed Mar 14 12:46:57 2018 -0400
@@ -0,0 +1,115 @@
+.. image:: https://travis-ci.org/abaizan/kodoja_galaxy.svg?branch=master
+   :alt: Linux testing with TravisCI
+   :target: https://travis-ci.org/abaizan/kodoja_galaxy/branches
+
+This is a Galaxy wrapper for the tool Kodoja, which is available to install in
+conda from bioconda.
+
+https://github.com/abaizan/kodoja
+
+Galaxy wrappers for Kodoja
+==========================
+
+These wrappers are copyright 2018 by Amanda Baizan Edge (University of
+St Andrews, and The James Hutton Institute) and Peter Cock (The James
+Hutton Institute). They are released under the MIT licence.
+
+These wrappers are available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/abaizan/kodoja
+
+In-development test releases are available from the Test Tool Shed at:
+http://testtoolshed.g2.bx.psu.edu/view/abaizan/kodoja
+
+
+Citation
+========
+
+Please refer to the main Kodoja citation instructions.
+
+
+Automated Installation
+======================
+
+Galaxy should be able to automatically install the dependencies, namely
+``kodoja`` and its dependencies like ``kraken`` and ``kaiju``, using the
+conda and the bioconda recipes.
+
+See the configuration notes below.
+
+
+Configuration
+=============
+
+You must tell Galaxy about any Kraken and Kaiju databases using configuration
+files ``kraken_databases.loc`` and ``kaiju_databases.loc`` which are located
+in the ``tool-data/`` folder. Sample files are included which explain the
+tab-based format to use.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.0  - Initial release covering ``kodoja_search.py`` v0.0.3.
+======= ======================================================================
+
+
+Bug Reports
+===========
+
+File a Galaxy wrapper issue at https://github.com/abaizan/kodoja_galaxy/issues
+
+For issues with Kodoja itself, use https://github.com/abaizan/kodoja/issues
+
+
+Developers
+==========
+
+For pushing a release to the test or main "Galaxy Tool Shed", use the
+following Planemo commands (which requires you have set your Tool Shed access
+details in ``~/.planemo.yml`` and that you have access rights on the Tool
+Shed)::
+
+    $ planemo shed_update -t testtoolshed --check_diff .
+    ...
+
+or::
+
+    $ planemo shed_update -t toolshed --check_diff .
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload -t testtoolshed --tar_only .
+    ...
+    $ tar -tzf shed_upload.tar.gz
+    LICENSE
+    README.rst
+    ...
+
+This simplifies ensuring a consistent set of files is bundled each time,
+including all the relevant test files.
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.