From 762dec393cf33d80674c5be4955eeeea5d1e5474 Mon Sep 17 00:00:00 2001
From: Konstantin Barsukov <konbarsukov@yandex.ru>
Date: Mon, 17 Dec 2018 13:11:56 +0300
Subject: [PATCH 1/2] Change '=' to '==' in wrapGSEA()

---
 pipeline_dfci.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pipeline_dfci.py b/pipeline_dfci.py
index ce34dae..e75c21d 100755
--- a/pipeline_dfci.py
+++ b/pipeline_dfci.py
@@ -5585,10 +5585,10 @@ def wrapGSEA(gctPath,clsPath,sample_1,sample_2,analysis_name,output_folder,metri
 
     IF YOU GET A STRANGE ERROR, MAKE SURE THE GENES IN YOUR GCT FILE ARE CAPITALIZED.
     '''
-    if gmxPath='':
+    if gmxPath=='':
         #default curated gene set
         gmxPath='/storage/cylin/grail/annotations/gsea/c2.all.v5.1.symbols.gmt'
-    if gseaPath='':
+    if gseaPath=='':
         #default gsea version
         gseaPath = '/storage/cylin/home/cl6/gsea2-3.0_beta_2.jar'
 

From c0c1bb26fa2d1f06f178d95cc3d15fb1a9df9713 Mon Sep 17 00:00:00 2001
From: Konstantin Barsukov <konstantin.barsukov@novartis.com>
Date: Thu, 27 Dec 2018 11:26:41 +0000
Subject: [PATCH 2/2] Add to geneMapper  _AllEnhancers.table.txt

---
 ROSE2_META.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/ROSE2_META.py b/ROSE2_META.py
index 5f25376..1faf218 100755
--- a/ROSE2_META.py
+++ b/ROSE2_META.py
@@ -748,9 +748,10 @@ def main():
     cmd = "python %sROSE2_geneMapper.py -g %s -i %s%s -f" % (pipeline_dir,genome, outFolder, superStretchTableFile)
     os.system(cmd)
 
-
-
-
+    allEnhancersTableFile = "%s_AllEnhancers.table.txt" % (inputName)
+    cmd = "python %sROSE2_geneMapper.py -g %s -i %s%s -f" % (pipeline_dir, genome, outFolder, allEnhancersTableFile)
+    print(cmd)
+    os.system(cmd)
 
 if __name__ == "__main__":
     main()