From 962813e50b53494badf038c31d6187a4a9bf3175 Mon Sep 17 00:00:00 2001
From: khalid belkhir <khalid.belkhir@univ-montp2.fr>
Date: Mon, 16 Dec 2019 09:11:41 +0100
Subject: [PATCH] Only One file
---
deployBigMem.sh | 67 +++++++++++++--------------
deployBigMemInterface.sh | 97 ----------------------------------------
2 files changed, 34 insertions(+), 130 deletions(-)
delete mode 100644 deployBigMemInterface.sh
diff --git a/deployBigMem.sh b/deployBigMem.sh
index ab34a90..11b6bf4 100644
--- a/deployBigMem.sh
+++ b/deployBigMem.sh
@@ -1,22 +1,14 @@
#!/bin/bash
#This script will help a deployment of a docker image on an MBB bigmem machine
-if [ $# -lt 1 ]
+
+if [ $# -lt 2 ]
then
- APP_IMG="mbbteam/rnaseqde:latest"
-else
- IMG_SRC=$1
- case $IMG_SRC in
- docker )
- APP_IMG="mbbteam/rnaseqde:latest" ;;
- local)
- docker build . -t rnaseqde:latest
- APP_IMG="rnaseqde:latest" ;;
- mbb)
- #APP_IMG="X.X.X.X:5000/rnaseqde:latest" ;;
- esac
+ echo usage : $0 dataDir resultsDir '[dockerHub|local]'
+ exit
fi
-
#nginx
+##### nginx install #####
+#sudo apt-get install -y nginx
# HOST_NAME="192.168.100.49"
@@ -60,37 +52,46 @@ then
fi
# Docker volumes
-#realUSER=$(who am i | awk '{print $1}')
-if [ $SUDO_USER ]; then realUSER=$SUDO_USER; else realUSER=`whoami`; fi
-VOL_DEV=/media/bigvol/$realUSER
# MBB Workflows reads data from /Data and write results to /Results
-mkdir -p ${VOL_DEV}/Data
-mkdir -p ${VOL_DEV}/Results
-DOCK_VOL+=" --mount type=bind,src=$VOL_DEV/Data,dst=/Data"
-DOCK_VOL+=" --mount type=bind,src=$VOL_DEV/Results,dst=/Results"
+if [ $SUDO_USER ]; then realUSER=$SUDO_USER; else realUSER=`whoami`; fi
+
+Data=$1
+Results=$2
+
+mkdir -p $Data
+mkdir -p $Results
+
+DOCK_VOL+=" --mount type=bind,src=$Data,dst=/Data"
+DOCK_VOL+=" --mount type=bind,src=$Results/Results,dst=/Results"
+
+if [ $# -lt 3 ]
+then
+ APP_IMG="mbbteam/radseqdenovo:latest"
+else
+ IMG_SRC=$3
+ case $IMG_SRC in
+ docker )
+ APP_IMG="mbbteam/radseqdenovo:latest" ;;
+ local)
+ docker build . -t radseqdenovo:latest
+ APP_IMG="radseqdenovo:latest" ;;
+ mbb)
+ #APP_IMG="X.X.X.X:5000/radseqdenovo:latest" ;;
+ esac
+fi
CONTAINER_ID=$( docker run --rm -d -p $APP_PORT:3838 $DOCK_VOL $APP_IMG )
if [ $CONTAINER_ID ]
then
echo " "
- echo You have to put your Data on : ${VOL_DEV}/Data
+ echo You have to put your Data on : $1
echo " "
- echo Results will be written to : ${VOL_DEV}/Results
+ echo Results will be written to : $2
echo " "
hostname -I | awk -v port=$APP_PORT '{print "You can access the workflow interface at : http://"$1":"port}'
echo " "
echo To start a Bash session inside the container : docker exec -it $CONTAINER_ID /bin/bash
- echo " "
- echo To run the workflow without the interface : docker exec -it $CONTAINER_ID snakemake -s /workflow/Snakefile all --configfile config --cores XX
- echo " "
- echo config est un fichier de configuration qui doit être dans un sous dossier de ${VOL_DEV}/Data ou ${VOL_DEV}/Results
- echo " "
- echo ex. si fichier dans ${VOL_DEV}/Data/run1/maconfig1.yml : docker exec -it $CONTAINER_ID snakemake -s /workflow/Snakefile all --configfile /Data/run1/maconfig1.yml --cores XX
- echo " "
- echo Vous pouvez utiliser l''interface graphique pour générer un fichier de configuration.
- echo " "
- echo XX étant le nombre de coeurs qui seront utilisés par le workflow.
else
echo Failed to run the docker container !!
fi
diff --git a/deployBigMemInterface.sh b/deployBigMemInterface.sh
deleted file mode 100644
index 11b6bf4..0000000
--- a/deployBigMemInterface.sh
+++ /dev/null
@@ -1,97 +0,0 @@
-#!/bin/bash
-#This script will help a deployment of a docker image on an MBB bigmem machine
-
-if [ $# -lt 2 ]
-then
- echo usage : $0 dataDir resultsDir '[dockerHub|local]'
- exit
-fi
-#nginx
-##### nginx install #####
-#sudo apt-get install -y nginx
-
- # HOST_NAME="192.168.100.49"
-
- # HTTP_ENDP="https://$HOST_NAME"
-
- # openssl req -x509 -nodes -days 365 -newkey rsa:2048 -keyout /etc/ssl/private/nginx-selfsigned.key -out /etc/ssl/certs/nginx-selfsigned.crt -subj "/C=FR/ST=LR/L=Montpellier/O=CNRS/OU=CNRS-ISEM/CN=mbb.univ-montp2.fr"
- # openssl dhparam -out /etc/ssl/certs/dhparam.pem 2048
-
- # mkdir -p /etc/nginx/snippets
- # echo "ssl_certificate /etc/ssl/certs/nginx-selfsigned.crt;" > /etc/nginx/snippets/self-signed.conf
- # echo "ssl_certificate_key /etc/ssl/private/nginx-selfsigned.key;" >> /etc/nginx/snippets/self-signed.conf
-
- # cp system/nginx_snippets_ssl-params.conf /etc/nginx/snippets/ssl-params.conf
-
- # cp /etc/nginx/sites-available/default /etc/nginx/sites-available/default.bak
-
- # cp system/nginx_sites-available_default /etc/nginx/sites-available/default
- # sed -i "s|server_domain_or_IP|$HOST_NAME|" /etc/nginx/sites-available/default
-
- # useradd nginx
- # cp system/nginx_nginx.conf /etc/nginx/nginx.conf
-
- # cp system/nginx_conf.d_10-rstudio.conf /etc/nginx/conf.d/10-rstudio.conf
- # sed -i "s|example.com|$HOST_NAME|" /etc/nginx/conf.d/10-rstudio.conf
-
- # systemctl restart nginx
- # systemctl enable nginx
-
-#essayer une plage de ports entre 8787 et 8800
-#APP_PORT=$2
-APP_PORT=8787
-while [[ $(ss -tulw | grep $APP_PORT) != "" && $APP_PORT < 8800 ]]
-do
- APP_PORT=$(( $APP_PORT + 1))
-done
-
-if [[ $(ss -tulw | grep $APP_PORT) != "" ]]
-then
- echo "No tcp port available !!"
- exit -1
-fi
-
-# Docker volumes
-# MBB Workflows reads data from /Data and write results to /Results
-
-if [ $SUDO_USER ]; then realUSER=$SUDO_USER; else realUSER=`whoami`; fi
-
-Data=$1
-Results=$2
-
-mkdir -p $Data
-mkdir -p $Results
-
-DOCK_VOL+=" --mount type=bind,src=$Data,dst=/Data"
-DOCK_VOL+=" --mount type=bind,src=$Results/Results,dst=/Results"
-
-if [ $# -lt 3 ]
-then
- APP_IMG="mbbteam/radseqdenovo:latest"
-else
- IMG_SRC=$3
- case $IMG_SRC in
- docker )
- APP_IMG="mbbteam/radseqdenovo:latest" ;;
- local)
- docker build . -t radseqdenovo:latest
- APP_IMG="radseqdenovo:latest" ;;
- mbb)
- #APP_IMG="X.X.X.X:5000/radseqdenovo:latest" ;;
- esac
-fi
-
-CONTAINER_ID=$( docker run --rm -d -p $APP_PORT:3838 $DOCK_VOL $APP_IMG )
-if [ $CONTAINER_ID ]
-then
- echo " "
- echo You have to put your Data on : $1
- echo " "
- echo Results will be written to : $2
- echo " "
- hostname -I | awk -v port=$APP_PORT '{print "You can access the workflow interface at : http://"$1":"port}'
- echo " "
- echo To start a Bash session inside the container : docker exec -it $CONTAINER_ID /bin/bash
-else
- echo Failed to run the docker container !!
-fi
--
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