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update README
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docs/README.rst

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@@ -85,14 +85,15 @@ install methylpy and run
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If you would like to install methylpy in path of your choice, run
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``python setup.py install --prefix=/USER/PATH/``. Then, try ``methylpy``
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and if it gives no error, the setup is likely successful. See `Test
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and if no error pops out, the setup is likely successful. See `Test
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methylpy <#test-methylpy>`__ for more rigorious test. Last, processing
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large dataset will require space for storing temporary files. However,
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the default directory is unlikely to fit the need. You may want to set
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the ``TMPDIR`` environmental variable to the absolute path of a
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directory on hard drive with sufficient space (e.g. ``/YOUR/TMP/DIR/``).
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This can be done by adding the below command to ~/.bashrc file:
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``export TMPDIR=/YOUR/TMP/DIR/``.
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large dataset will require large spare space for temporary files.
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Usually, the default directory for temporary files will not meet the
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need. You may want to set the ``TMPDIR`` environmental variable to the
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(absolute) path of a directory on hard drive with sufficient space (e.g.
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``/YOUR/TMP/DIR/``). This can be done by adding the below command to
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``~/.bashrc file``: ``export TMPDIR=/YOUR/TMP/DIR/`` and run
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``source ~/.bashrc``.
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Step 2 - Install dependencies
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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::
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cd methylpy/test
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wget http://neomorph.salk.edu/yupeng/share/methylpy_test.tar.gz
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tar -xf methylpy_test.tar.gz
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cd methylpy_test/
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python run_test.py
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The test should take around 3 minutes, and progress will be printed on
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screen. After the test is started, two files ``test_output_msg.txt`` and
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``test_error_msg.txt`` will be generated. The former contains more
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details about each test and the later stores error message (if any) as
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well as additional information.
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If test fails, please check ``test_error_msg.txt`` for the error
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message. If you decide to submit an issue regarding test failure to
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methylpy github page, please include the error message in this file.
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Process data
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============
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setup.py

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setup(
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name='methylpy',
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version='1.2.3',
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version='1.2.4',
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author='Yupeng He',
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author_email='yupeng.he.bioinfo@gmail.com',
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packages=['methylpy'],

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