@@ -85,14 +85,15 @@ install methylpy and run
8585
8686If you would like to install methylpy in path of your choice, run
8787``python setup.py install --prefix=/USER/PATH/ ``. Then, try ``methylpy ``
88- and if it gives no error, the setup is likely successful. See `Test
88+ and if no error pops out , the setup is likely successful. See `Test
8989methylpy <#test-methylpy> `__ for more rigorious test. Last, processing
90- large dataset will require space for storing temporary files. However,
91- the default directory is unlikely to fit the need. You may want to set
92- the ``TMPDIR `` environmental variable to the absolute path of a
93- directory on hard drive with sufficient space (e.g. ``/YOUR/TMP/DIR/ ``).
94- This can be done by adding the below command to ~/.bashrc file:
95- ``export TMPDIR=/YOUR/TMP/DIR/ ``.
90+ large dataset will require large spare space for temporary files.
91+ Usually, the default directory for temporary files will not meet the
92+ need. You may want to set the ``TMPDIR `` environmental variable to the
93+ (absolute) path of a directory on hard drive with sufficient space (e.g.
94+ ``/YOUR/TMP/DIR/ ``). This can be done by adding the below command to
95+ ``~/.bashrc file ``: ``export TMPDIR=/YOUR/TMP/DIR/ `` and run
96+ ``source ~/.bashrc ``.
9697
9798Step 2 - Install dependencies
9899^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -158,9 +159,21 @@ correctly, run
158159
159160::
160161
161- cd methylpy/test
162+ wget http://neomorph.salk.edu/yupeng/share/methylpy_test.tar.gz
163+ tar -xf methylpy_test.tar.gz
164+ cd methylpy_test/
162165 python run_test.py
163166
167+ The test should take around 3 minutes, and progress will be printed on
168+ screen. After the test is started, two files ``test_output_msg.txt `` and
169+ ``test_error_msg.txt `` will be generated. The former contains more
170+ details about each test and the later stores error message (if any) as
171+ well as additional information.
172+
173+ If test fails, please check ``test_error_msg.txt `` for the error
174+ message. If you decide to submit an issue regarding test failure to
175+ methylpy github page, please include the error message in this file.
176+
164177Process data
165178============
166179
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