From 470c53839313820a3dff6d6f77c3976b8aa04019 Mon Sep 17 00:00:00 2001
From: khalid belkhir <khalid.belkhir@univ-montp2.fr>
Date: Tue, 17 Dec 2019 09:59:42 +0100
Subject: [PATCH] IMG src to dockerHub
---
RunCmdLine.sh | 8 +++++---
deployBigMem.sh | 2 +-
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/RunCmdLine.sh b/RunCmdLine.sh
index a6bde6e..9830601 100644
--- a/RunCmdLine.sh
+++ b/RunCmdLine.sh
@@ -6,6 +6,7 @@ then
echo usage : $0 dataDir resultsDir configFile nbCores '[dockerHub|local]'
exit
fi
+
# Docker volumes
# MBB Workflows reads data from /Data and write results to /Results
@@ -33,7 +34,7 @@ then
else
IMG_SRC=$5
case $IMG_SRC in
- docker )
+ dockerHub )
APP_IMG="mbbteam/rnaseqde:latest" ;;
local)
docker build . -t rnaseqde:latest
@@ -43,12 +44,13 @@ else
esac
fi
-CONTAINER_ID=$( docker run --rm $DOCK_VOL $APP_IMG snakemake -s /workflow/Snakefile all --configfile $config --cores $cores)
+docker run --rm $DOCK_VOL --cidfile="CID.txt" $APP_IMG snakemake -s /workflow/Snakefile all --configfile $config --cores $cores
+CONTAINER_ID=$(cat CID.txt)
if [ $CONTAINER_ID ]
then
echo " "
- echo Results were written to : $3
+ echo Results were written to : $2
echo " "
else
echo Failed to run the docker container !!
diff --git a/deployBigMem.sh b/deployBigMem.sh
index bd0661a..2bffc94 100644
--- a/deployBigMem.sh
+++ b/deployBigMem.sh
@@ -71,7 +71,7 @@ then
else
IMG_SRC=$3
case $IMG_SRC in
- docker )
+ dockerHub )
APP_IMG="mbbteam/rnaseqde:latest" ;;
local)
docker build . -t rnaseqde:latest
--
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