upgrade installation

hitbc · Sep 24, 2019 · 8c92ce5 · 8c92ce5
1 parent 487bcd6
commit 8c92ce5
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Showing 15 changed files with 17 additions and 22 deletions.
diff --git a/INSTALL.sh b/INSTALL.sh
diff --git a/README.md b/README.md
@@ -13,8 +13,7 @@ rMETL - realignment-based Mobile Element insertion detection Tool for Long read
 
 	$ git clone https://github.com/tjiangHIT/rMETL.git (git clone https://github.com/hitbc/rMETL.git)
 	$ cd rMETL/
-	$ bash INSTALL.sh
-	$ ./rMETL.py
+	$ pip install .
 
 ---	
 ### Introduction

diff --git a/src/rMETL/rMETL b/src/rMETL/rMETL
@@ -11,10 +11,10 @@
 '''
 
 import argparse
-import rMETL_extraction
-import rMETL_realign
-import rMETL_MEIcalling
-from rMETL_version import __version__, __author__, __contact__
+import rMETL.rMETL_extraction as rMETL_extraction
+import rMETL.rMETL_realign as rMETL_realign
+import rMETL.rMETL_MEIcalling as rMETL_MEIcalling
+from rMETL.rMETL_version import __version__, __author__, __contact__
 
 STAGES = {'detection': rMETL_extraction.run, \
           'realignment': rMETL_realign.run, \

diff --git a/src/rMETL/rMETL_MEIcalling.py b/src/rMETL/rMETL_MEIcalling.py
@@ -17,10 +17,10 @@
 import cigar
 
 from collections import Counter
-from rMETL_version import __version__, __author__, __contact__
-from rMETL_genotype import simple_call_genotype
-from rMETL_cmdRunner import setupLogging
-from rMETL_utils import load_ref
+from rMETL.rMETL_version import __version__, __author__, __contact__
+from rMETL.rMETL_genotype import simple_call_genotype
+from rMETL.rMETL_cmdRunner import setupLogging
+from rMETL.rMETL_utils import load_ref
 
 USAGE="""\
            _  ___  _   _____   _______   _

diff --git a/src/rMETL/rMETL_MEIcalling.pyc b/src/rMETL/rMETL_MEIcalling.pyc
diff --git a/src/rMETL/rMETL_cmdRunner.pyc b/src/rMETL/rMETL_cmdRunner.pyc
diff --git a/src/rMETL/rMETL_concensus.pyc b/src/rMETL/rMETL_concensus.pyc
diff --git a/src/rMETL/rMETL_extraction.py b/src/rMETL/rMETL_extraction.py
@@ -20,11 +20,11 @@
 import gc
 
 from multiprocessing import Pool
-from rMETL_version import __version__, __author__, __contact__
-from rMETL_concensus import construct_concensus_info
-from rMETL_genotype import add_genotype
-from rMETL_utils import load_ref, check_bai, call_ngmlr, call_samtools
-from rMETL_cmdRunner import setupLogging, exe
+from rMETL.rMETL_version import __version__, __author__, __contact__
+from rMETL.rMETL_concensus import construct_concensus_info
+from rMETL.rMETL_genotype import add_genotype
+from rMETL.rMETL_utils import load_ref, check_bai, call_ngmlr, call_samtools
+from rMETL.rMETL_cmdRunner import setupLogging, exe
 
 USAGE="""\
            _  ___  _   _____   _______   _

diff --git a/src/rMETL/rMETL_extraction.pyc b/src/rMETL/rMETL_extraction.pyc
diff --git a/src/rMETL/rMETL_genotype.pyc b/src/rMETL/rMETL_genotype.pyc
diff --git a/src/rMETL/rMETL_realign.py b/src/rMETL/rMETL_realign.py
@@ -15,8 +15,8 @@
 import sys
 import time
 
-from rMETL_version import __version__, __author__, __contact__
-from rMETL_cmdRunner import setupLogging, exe
+from rMETL.rMETL_version import __version__, __author__, __contact__
+from rMETL.rMETL_cmdRunner import setupLogging, exe
 
 USAGE="""\
            _  ___  _   _____   _______   _

diff --git a/src/rMETL/rMETL_realign.pyc b/src/rMETL/rMETL_realign.pyc
diff --git a/src/rMETL/rMETL_utils.py b/src/rMETL/rMETL_utils.py
@@ -4,7 +4,7 @@
 import logging
 import os
 from Bio import SeqIO
-from rMETL_cmdRunner import exe
+from rMETL.rMETL_cmdRunner import exe
 
 def load_ref(ref_g):
 	logging.info("Loading reference genome...")

diff --git a/src/rMETL/rMETL_utils.pyc b/src/rMETL/rMETL_utils.pyc
diff --git a/src/rMETL/rMETL_version.pyc b/src/rMETL/rMETL_version.pyc