Merge branch 'master' of forgemia.inra.fr:svdetection/cnvpipelines

.gitmodules

 [submodule "snakecnv/lib"]
 	path = snakecnv/lib
-	url = git@forgemia.inra.fr:svdetection/svlib.git
-        branch=master
+	url = https://forgemia.inra.fr/svdetection/svlib.git
+    branch = master
 [submodule "popsim"]
 	path = popsim
-	url = git@forgemia.inra.fr:svdetection/popsim.git
+	url = https://forgemia.inra.fr/svdetection/popsim.git
 	branch = master

popsim @ 5178e983

-Subproject commit e3f393cdd41ae8aa91f9df635cc602583c2da2be
+Subproject commit 5178e983dae01040b6c82624d0e28990975ccd7c

snakecnv/common.smk

-
 import os
 import sys
 from termcolor import cprint
@@ -12,7 +11,7 @@ import pysam
 # TODO shouldn't this be defined elsewhere ?
 ROOTPATH = os.path.dirname(workflow.snakefile)
 shell.prefix("export PATH=%s/bin:\"$PATH\";" % ROOTPATH)
-os.environ["PYTHONPATH"] = os.path.join(ROOTPATH, "../popsim/svlib")
+os.environ["PYTHONPATH"] = os.path.join(ROOTPATH, "lib")
 
 # For each tool the list of sv that can be detected
 # FIXME organize this differently