From 7ce2b1a9c687377c7a4a2945d0562aa43848158d Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 19 Jun 2018 14:30:12 -0500
Subject: [PATCH] Fix scripts.
---
workflow/conf/biohpc.config | 2 +-
workflow/scripts/map_qc.py | 2 +-
workflow/scripts/overlap_peaks.py | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 21a5343..df20dd9 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -70,7 +70,7 @@ params {
tssfile = '/project/shared/bicf_workflow_ref/GRCh38/gencode.tss'
}
'GRCm38' {
- git'
+ bwa = '/project/shared/bicf_workflow_ref/GRCm38'
genomesize = 'mm'
chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
tssfile = '/project/shared/bicf_workflow_ref/GRCh38/gencode.tss'
diff --git a/workflow/scripts/map_qc.py b/workflow/scripts/map_qc.py
index 5bb74f0..d58ae8f 100644
--- a/workflow/scripts/map_qc.py
+++ b/workflow/scripts/map_qc.py
@@ -10,7 +10,7 @@ import shlex
import logging
from multiprocessing import cpu_count
import pandas as pd
-from python_utils import utils
+import utils
EPILOG = '''
diff --git a/workflow/scripts/overlap_peaks.py b/workflow/scripts/overlap_peaks.py
index 61f7ac5..514b13d 100644
--- a/workflow/scripts/overlap_peaks.py
+++ b/workflow/scripts/overlap_peaks.py
@@ -8,7 +8,7 @@ import logging
import shutil
import pandas as pd
import sys
-from python_utils import utils
+import utils
EPILOG = '''
For more details:
--
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