diff README.rst @ 0:06cb587a5e87 draft

Uploaded initial version 2.1.0-4.

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+MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1.0) peak calling
+==================================================================
+
+Galaxy tool wrapper for the peak calling function of MACS 2.1.0. MACS has been
+developed by Tao Lui
+https://github.com/taoliu/MACS/
+
+The reference for MACS is:
+
+- Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers
+  RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol.
+  2008;9(9):R137
+
+Automated installation
+======================
+
+Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
+the MACS 2.1.0 program.
+
+Manual Installation
+===================
+
+There are two files to install:
+
+- ``macs21_wrapper.xml`` (the Galaxy tool definition)
+- ``macs21_wrapper.py.sh`` (the Python script wrapper)
+
+The suggested location is in a ``tools/macs21/`` folder. You will then
+need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
+by adding the line:
+
+    <tool file="macs21/macs21_wrapper.xml" />
+
+You will also need to install MACS 2.1.0 and its dependencies:
+
+- https://pypi.python.org/pypi/MACS2
+
+and ensure that it's on your Galaxy user's ``PATH`` when running the tool.
+
+If you want to run the functional tests, copy the sample test files under
+sample test files under Galaxy's ``test-data/`` directory. Then:
+
+    ./run_tests.sh -id macs2_wrapper
+
+
+History
+=======
+
+This tool was originally based on the ``modencode-dcc`` MACS2 tool developed
+by Ziru Zhou ([e-mail]), specifically the ``16:14f378e35191``
+revision of the tool available via
+
+- http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 
+
+This version has been substantially modified both to adapt it to MACS 2.1.0, and
+to re-implement the internal workings of the tool to conform with current
+practices in invoking commands from Galaxy, and to add new functionality.
+
+========== ======================================================================
+Version    Changes
+---------- ----------------------------------------------------------------------
+2.1.0-4    - Remove 'bdgcmp' functionality.
+2.1.0-3    - Add tool tests
+2.1.0-2    - Add option to create bigWig file from bedGraphs; fix bug with -B
+             option; make --mfold defaults consistent.
+2.1.0-1    - Initial version
+========== ======================================================================
+
+
+Developers
+==========
+
+This tool is developed on the following GitHub repository:
+https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/macs21
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
+the ``package_macs21_wrapper.sh`` script.
+
+
+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.