test setup.py

hitbc · Sep 24, 2019 · 487bcd6 · 487bcd6
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Showing 20 changed files with 14 additions and 12 deletions.
diff --git a/INSTALL.sh b/INSTALL.sh
@@ -1,4 +1,4 @@
 # !/usr/bin/bash
 
-ln -s src/rMETL.py rMETL.py
+ln -s src/rMETL/rMETL rMETL
 
diff --git a/setup.py b/setup.py
@@ -2,14 +2,14 @@
 
 from setuptools import setup, find_packages
 
-LONG_DESCRIPTION = '''Mobile element insertion (MEI) is a major category of structure variations (SVs). 
-The rapid development of long read sequencing provides the opportunity to sensitively discover MEIs. 
-However, the signals of MEIs implied by noisy long reads are highly complex, due to the repetitiveness 
-of mobile elements as well as the serious sequencing errors. Herein, we propose Realignment-based 
-Mobile Element insertion detection Tool for Long read (rMETL). rMETL takes advantage of 
-its novel chimeric read re-alignment approach to well handle complex MEI signals. 
-Benchmarking results on simulated and real datasets demonstrated that rMETL has the ability 
-to more sensitivity discover MEIs as well as prevent false positives. 
+LONG_DESCRIPTION = '''Mobile element insertion (MEI) is a major category of structure variations (SVs). \
+The rapid development of long read sequencing provides the opportunity to sensitively discover MEIs. \
+However, the signals of MEIs implied by noisy long reads are highly complex, due to the repetitiveness \
+of mobile elements as well as the serious sequencing errors. Herein, we propose Realignment-based \
+Mobile Element insertion detection Tool for Long read (rMETL). rMETL takes advantage of \
+its novel chimeric read re-alignment approach to well handle complex MEI signals. \
+Benchmarking results on simulated and real datasets demonstrated that rMETL has the ability \
+to more sensitivity discover MEIs as well as prevent false positives. \
 It is suited to produce high quality MEI callsets in many genomics studies.'''
 
 setup(
@@ -19,9 +19,11 @@
     author = "Jiang Tao",
     author_email = "[email protected]",
     url = "https://github.com/tjiangHIT/rMETL",
-    license = "MIT Licence",
-    packages = find_packages('src'),
-    package_dir = {'': 'src'},
+    license = "MIT",
+    packages = find_packages("src"),
+    package_dir = {"": "src"},
+    data_files = [("", ["LICENSE"])],
+    scripts=['src/rMETL/rMETL'],
     long_description = LONG_DESCRIPTION,
     zip_safe = False,
     install_requires = ['pysam', 'Biopython', 'Cigar']

diff --git a/src/__init__.py → src/rMETL/__init__.py b/src/__init__.py → src/rMETL/__init__.py
diff --git a/src/rMETL.py → src/rMETL/rMETL b/src/rMETL.py → src/rMETL/rMETL
diff --git a/src/rMETL_MEIcalling.py → src/rMETL/rMETL_MEIcalling.py b/src/rMETL_MEIcalling.py → src/rMETL/rMETL_MEIcalling.py
diff --git a/src/rMETL/rMETL_MEIcalling.pyc b/src/rMETL/rMETL_MEIcalling.pyc
diff --git a/src/rMETL_cmdRunner.py → src/rMETL/rMETL_cmdRunner.py b/src/rMETL_cmdRunner.py → src/rMETL/rMETL_cmdRunner.py
diff --git a/src/rMETL/rMETL_cmdRunner.pyc b/src/rMETL/rMETL_cmdRunner.pyc
diff --git a/src/rMETL_concensus.py → src/rMETL/rMETL_concensus.py b/src/rMETL_concensus.py → src/rMETL/rMETL_concensus.py
diff --git a/src/rMETL/rMETL_concensus.pyc b/src/rMETL/rMETL_concensus.pyc
diff --git a/src/rMETL_extraction.py → src/rMETL/rMETL_extraction.py b/src/rMETL_extraction.py → src/rMETL/rMETL_extraction.py
diff --git a/src/rMETL/rMETL_extraction.pyc b/src/rMETL/rMETL_extraction.pyc
diff --git a/src/rMETL_genotype.py → src/rMETL/rMETL_genotype.py b/src/rMETL_genotype.py → src/rMETL/rMETL_genotype.py
diff --git a/src/rMETL/rMETL_genotype.pyc b/src/rMETL/rMETL_genotype.pyc
diff --git a/src/rMETL_realign.py → src/rMETL/rMETL_realign.py b/src/rMETL_realign.py → src/rMETL/rMETL_realign.py
diff --git a/src/rMETL/rMETL_realign.pyc b/src/rMETL/rMETL_realign.pyc
diff --git a/src/rMETL_utils.py → src/rMETL/rMETL_utils.py b/src/rMETL_utils.py → src/rMETL/rMETL_utils.py
diff --git a/src/rMETL/rMETL_utils.pyc b/src/rMETL/rMETL_utils.pyc
diff --git a/src/rMETL_version.py → src/rMETL/rMETL_version.py b/src/rMETL_version.py → src/rMETL/rMETL_version.py
diff --git a/src/rMETL/rMETL_version.pyc b/src/rMETL/rMETL_version.pyc