Commit a4024940 authored by Antony Le Béchec's avatar Antony Le Béchec

Merge branch '0.9.18.2'

parents 5324ee33 1828b92a
......@@ -200,7 +200,9 @@ def get_sample_id_from_samplesheet(samplesheetPath):
with open(samplesheetPath, "r") as f:
for l in f:
if not inDataTable:
if l.startswith("Sample_ID,Sample_Name,"):
#modif JB
#if l.startswith("Sample_ID,Sample_Name,"):
if l.startswith("Sample_ID,"):
inDataTable = True
sampleIDIndex = l.strip().split(",").index("Sample_ID")
else:
......@@ -297,6 +299,8 @@ def copyAllResults(output, exclude):
sample_list = []
sample_list = get_sample_id_from_samplesheet(find_any_samplesheet(output))
results = osj("/app",os.path.basename(os.path.normpath(output)))
if os.path.exists(osj(output,".snakemake/")):
shutil.rmtree(osj(output,".snakemake/"))
if not sample_list:
# command = 'find '+output+'/*/CANOES/*.canoes.annotsv.tsv'
command = 'find '+osj(results,"*/CANOES/*.canoes.annotsv.tsv")
......@@ -313,8 +317,6 @@ def copyAllResults(output, exclude):
shutil.copytree(osj(results,"logs/"),osj(output,sample,"CANOES/logs"))
# if os.path.exists(osj(output,"CANOES/")):
# shutil.rmtree(osj(output,"CANOES/"))
if os.path.exists(osj(output,".snakemake/")):
shutil.rmtree(osj(output,".snakemake/"))
# if os.path.exists(osj(output,"logs/")):
# shutil.rmtree(osj(output,"logs/"))
# if os.path.exists(output+"/Rplots.pdf"):
......
......@@ -144,7 +144,7 @@ DOCKER_STARK_MODULE_SUBMODULE_SERVICE_LISTENER_INNER_FOLDER_SERVICES=${DOCKER_ST
# LISTENER service parameters
DOCKER_STARK_MODULE_SUBMODULE_SERVICE_LISTENER_PARAM_SLEEP=600
DOCKER_STARK_MODULE_SUBMODULE_SERVICE_LISTENER_PARAM_DAEMON_RUN_EXISTENCE=120
DOCKER_STARK_MODULE_SUBMODULE_SERVICE_LISTENER_PARAM_DAEMON_RUN_EXISTENCE=700
DOCKER_STARK_MODULE_SUBMODULE_SERVICE_LISTENER_PARAM_DAEMON_DELAY=0
DOCKER_STARK_MODULE_SUBMODULE_NAME_LISTENER=VARANK
DOCKER_STARK_MODULE_SUBMODULE_SERVICE_LISTENER_PARAM_MICROSERVICE_NAME=VARANK
......
......@@ -63,7 +63,7 @@ RUN mkdir /tools; \
ln -s VaRank_1.4.3 current; \
cd current/ExtAnn; \
rm -f OMIMannotations.tsv.gz; \
ln -s /STARK/databases/OMIMannotations/current/OMIMannotations.tsv.gz ./OMIMannotations.tsv.gz
ln -s /STARK/databases/OMIMannotations/current/OMIMannotations.tsv.gz /tools/varank/current/ExtAnn/OMIMannotations.tsv.gz
ARG VARANK=/tools/varank/current/
ENV VARANK $VARANK
......
../../../common/listener/listener/dockerfile/
\ No newline at end of file
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