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+Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
+==========================================================
+
+This wrapper is copyright 2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+CLC Assembly Cell is the commercial command line assembly suite from CLCbio.
+It uses SIMD instructions to parallelize and accelerate their assembly
+algorithms, and is also very memory efficient making it an appealing choice
+for complex genomes where the RAM requirements exclude other popular tools.
+
+For more information:
+http://www.clcbio.com/products/clc-assembly-cell/
+
+You can download the CLC Assembly Cell User Manual here, currently v4.2
+http://www.clcbio.com/files/usermanuals/CLC_Assembly_Cell_User_Manual.pdf
+
+There is also an online manual here:
+http://clcsupport.com/clcassemblycell/current/index.php?manual=Introduction.html
+
+There is currently a free trial download here:
+http://www.clcbio.com/?action=transfer_user&productVersion=4.2&productID=6982&productName=CLC+Assembly+Cell&nonce=db842e3f95
+
+This wrapper is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
+
+This Galaxy wrapper was written and tested using CLC Assembly Cell
+version 4.10.86742
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and
+install the wrapper from the Galaxy Tool Shed. However, you will need to
+manually install the CLC Assembly Cell software, and setup the environment
+variable ``$CLC_ASSEMBLY_CELL`` to the directory containing the binaries
+(and in particular, the ``clc_assembler`` binary). For example:
+
+$ export CLC_ASSEMBLY_CELL=/opt/clcbio/clc-assembly-cell-4.1.0-linux_64/
+
+
+Manual Installation
+===================
+
+First install the CLC Assembly Cell sortware as described above.
+
+To install the wrapper copy or move the following files under the Galaxy tools
+folder, e.g. in a ``tools/clcbio/`` folder:
+
+* clc_assembler.xml (Galaxy tool definition)
+* clc_mapper.xml (Galaxy tool definition)
+* README.rst (this file)
+
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
+the tools. Just all these line, for example next to other assembly tools::
+
+  <tool file="clc_assembly_cell/clc_assembler.xml" />
+  <tool file="clc_assembly_cell/clc_mapper.xml" />
+
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then run::
+
+    $ ./run_tests.sh -id clc_assembler
+    $ ./run_tests.sh -id clc_mapper
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial public release.
+v0.0.2  - Actually use the ``$CLC_ASSEMBLY_CELL`` environment variable.
+        - Enable and fixed the tests.
+======= ======================================================================
+
+
+Developers
+==========
+
+Development is on this itHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf clcbio.tar.gz tools/clc_assembly_cell/README.rst tools/clc_assembly_cell/clc_assembler.xml tools/clc_assembly_cell/clc_mapper.xml tools/clc_assembly_cell/tool_dependencies.xml test-data/NC_010642.fna
+
+Check this worked::
+
+    $ tar -tzf clcbio.tar.gz
+    tools/clc_assembly_cell/README.rst
+    tools/clc_assembly_cell/clc_assembler.xml
+    tools/clc_assembly_cell/clc_mapper.xml
+    tools/clc_assembly_cell/tool_dependencies.xml
+    test-data/NC_010642.fna
+
+
+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.
+
+NOTE: This is the licence for the Galaxy Wrapper only. The CLCbio tools are
+commercial, and are available and licenced separately.