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Commit b20386b9 authored by Thomas Faraut's avatar Thomas Faraut
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Merge branch 'master' of forgemia.inra.fr:svdetection/cnvpipelines

parents 72d1439d 5e06f4a8
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[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
Subproject commit e3f393cdd41ae8aa91f9df635cc602583c2da2be
Subproject commit 5178e983dae01040b6c82624d0e28990975ccd7c
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
......
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