Add deploy scripts

Update containers recipes for ISEM and MBB clusters

Genome_Profile/Dockerfile

@@ -17,5 +17,19 @@ RUN cd /opt/biotools \
  && mv genomescope-1.0.0/genomescope.R . \
  && rm -r genomescope-1.0.0 genomescope.tar.gz
 
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US:en
+ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin  
+&& mkdir /share/apps/lib  
+&& mkdir /share/apps/gridengine  
+&& mkdir /share/bio  
+&& mkdir -p /opt/gridengine  
+&& mkdir -p /export/scrach  
+&& mkdir -p /usr/lib64  
+&& ln -s /bin/bash /bin/mbb_bash     
+&& ln -s /bin/bash /bin/isem_bash  
+&& /usr/sbin/groupadd --system --gid 400 sge  
+&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
+
 EXPOSE 3838
 CMD ["Rscript", "-e", "setwd('/sagApp/'); shiny::runApp('/sagApp/app.R',port=3838 , host='0.0.0.0')"]

Genome_Profile/deploy.sh

+#!/bin/bash
+
+# This script is executed on the virtual machine during the *Deployment* phase.
+# It is used to apply parameters specific to the current deployment.
+# It is executed secondly during a cloud deployement in IFB-Biosphere, after the *Installation* phase.
+if [ $# -lt 1 ]
+then
+    APP_IMG="mbbteam/genome_profile:latest"  
+else 
+    IMG_SRC=$1
+    case $IMG_SRC in
+        ifb)
+            APP_IMG="gitlab-registry.in2p3.fr/ifb-biosphere/apps/genome_profile:master" ;;
+        docker )
+            APP_IMG="mbbteam/genome_profile:latest"  ;;
+        local)
+            docker build . -t genome_profile:latest 
+            APP_IMG="genome_profile:latest" ;;
+        mbb)    
+            #APP_IMG="X.X.X.X:5000/genome_profile:latest" ;;
+    esac
+fi
+
+
+# Tuning if site proxy or not
+#CLOUD_SERVICE = $(ss-get cloudservice)
+#CLOUD_SERVICE="ifb-genouest-genostack"
+
+#HOST_NAME=$( ss-get --timeout=3 hostname )
+HOST_NAME="192.168.100.49"
+#if [ "$CLOUD_SERVICE" == "ifb-genouest-genostack" ]; then
+    # Cloud site WITH a site proxy
+#    APP_PORT=80
+#    PROXIED_IP=$( echo $HOST_NAME | sed "s|\.|-|g")
+#    HOST_NAME="openstack-${PROXIED_IP}.genouest.org"
+#    HTTP_ENDP="https://$HOST_NAME"
+
+#    systemctl stop nginx
+#else
+    # Cloud site WOUT a site proxy
+    APP_PORT=8787
+    HTTP_ENDP="https://$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=AURA/L=Lyon/O=IFB/OU=IFB-biosphere/CN=myrstudio.biosphere.france-bioinformatique.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
+#fi
+
+# Docker volumes
+
+# mydatalocal: from the system disk or ephemeral  one
+IFB_DATADIR="/ifb/data/"
+source /etc/profile.d/ifb.sh
+VOL_NAME="mydatalocal"
+VOL_DEV=$(readlink -f -n $IFB_DATADIR/$VOL_NAME )
+DOCK_VOL=" --mount type=bind,src=$VOL_DEV,dst=$IFB_DATADIR/$VOL_NAME"
+
+# MBB Workflows reads data from /Data and write results to /Results
+mkdir ${VOL_DEV}/Data
+mkdir ${VOL_DEV}/Results
+DOCK_VOL+=" --mount type=bind,src=$VOL_DEV/Data,dst=/Data"
+DOCK_VOL+=" --mount type=bind,src=$VOL_DEV/Results,dst=/Results"
+
+# NFS mounts: from ifb_share configuration in autofs
+IFS_ORI=$IFS
+while IFS=" :" read VOL_NAME VOL_TYPE VOL_IP VOL_DEV ; do
+        DOCK_VOL+=" --mount type=volume,volume-driver=local,volume-opt=type=nfs,src=$VOL_NAME,dst=$IFB_DATADIR/$VOL_NAME,volume-opt=device=:$VOL_DEV,volume-opt=o=addr=$VOL_IP"
+done < /etc/auto.ifb_share
+IFS=$IFS_ORI
+
+
+
+CONTAINER_ID=$( docker run -d -p $APP_PORT:3838 $DOCK_VOL $APP_IMG )
+
+VM_IP=$(curl bot.whatismyipaddress.com)
+
+if [ $CONTAINER_ID ]
+then
+    echo " "
+    echo You have to put your Data on  : ${VOL_DEV}/Data
+    echo " "
+    echo Results will be written to    : ${VOL_DEV}/Results
+    echo " "
+    echo You can access the workflow interface at :  https://${VM_IP}
+    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
\ No newline at end of file

Genome_Profile/deployBigMem.sh

+#!/bin/bash
+#This script will help a deployment of a docker image on an MBB bigmem machine
+if [ $# -lt 1 ]
+then
+    APP_IMG="mbbteam/genome_profile:latest"  
+else 
+    IMG_SRC=$1
+    case $IMG_SRC in
+        docker )
+            APP_IMG="mbbteam/genome_profile:latest"  ;;
+        local)
+            docker build . -t genome_profile:latest 
+            APP_IMG="genome_profile:latest" ;;
+        mbb)    
+            #APP_IMG="X.X.X.X:5000/genome_profile:latest" ;;
+    esac
+fi
+
+#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 $APP_PORT) != "" ]]
+then
+  echo "No tcp port available !!"
+  exit -1
+fi
+
+# Docker volumes
+#realUSER=$(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=$VOL_DEV/Results,dst=/Results"
+
+
+CONTAINER_ID=$( 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 " "
+    echo Results will be written to    : ${VOL_DEV}/Results
+    echo " "
+    hostname -I | awk -v port=$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
\ No newline at end of file

Genome_Profile/files/singularity.def

@@ -5,8 +5,9 @@ From: ../base.sif
 	export PATH=/opt/biotools/bin:$PATH
 	export ROOTSYS=/opt/biotools/root
 	export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'
-	
-
+	export LANG=en_US.UTF-8
+export LANGUAGE=en_US:en
+export LC_ALL=en_US.UTF-8
 
 %labels
 	Author YourName
@@ -95,3 +96,14 @@ singularity run --app appName this_container.sif
 	mv genomescope-1.0.0/genomescope.R .
 	rm -r genomescope-1.0.0 genomescope.tar.gz
 
+mkdir -p /share/apps/bin
+mkdir /share/apps/lib
+mkdir /share/apps/gridengine
+mkdir /share/bio
+mkdir -p /opt/gridengine
+mkdir -p /export/scrach
+mkdir -p /usr/lib64
+ln -s /bin/bash /bin/mbb_bash   
+ln -s /bin/bash /bin/isem_bash
+/usr/sbin/groupadd --system --gid 400 sge
+/usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
\ No newline at end of file

Genome_Profile/install.sh

+##### nginx install #####
+sudo apt-get install -y nginx
\ No newline at end of file

Genome_Profile/waw_workflow.qsub

+#!/bin/bash 
+#$ -S /bin/bash 
+# Job name 
+#$ -N WAW_worflow 
+# Using current working directory (otherwise, you will have to use '#$ wd /path/to/run') 
+#$ -cwd 
+# job time limits (h_rt is required [s_rt == software time limit / h_rt == hardware time limit]) 
+#$ -l h_rt=48:00:00 
+# Redirects the standard output to the named file. 
+#$ -o Results/waw.out 
+#$ -e Results/waw.err 
+module load singularity-3.1 
+
+dataDir=$1
+resultsDir=$2
+# Config file in a location binded to /Data or /Results 
+#ex. file in /home/khalid/dataanalyse/config.yaml
+#/home/khalid/dataanalyse/ is dataDir thet will be binded to /Data in the container
+#configfile must be set to /Data/config.yaml
+configFile=$3 
+cores=$4
+#if we must build the image from docker image
+singularity build genome_profile.simg docker://mbbteam/genome_profile:latest
+
+
+#Run the workflow in cmd line
+singularity exec -B $dataDir:/Data -B $resultsDir:/Results genome_profile.simg snakemake  -s /workflow/Snakefile --configfile $configFile --cores $cores

Interop_report/Dockerfile

@@ -11,5 +11,19 @@ RUN cd /opt/biotools \
 
 RUN apt install -y gnuplot
 
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US:en
+ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin  
+&& mkdir /share/apps/lib  
+&& mkdir /share/apps/gridengine  
+&& mkdir /share/bio  
+&& mkdir -p /opt/gridengine  
+&& mkdir -p /export/scrach  
+&& mkdir -p /usr/lib64  
+&& ln -s /bin/bash /bin/mbb_bash     
+&& ln -s /bin/bash /bin/isem_bash  
+&& /usr/sbin/groupadd --system --gid 400 sge  
+&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
+
 EXPOSE 3838
 CMD ["Rscript", "-e", "setwd('/sagApp/'); shiny::runApp('/sagApp/app.R',port=3838 , host='0.0.0.0')"]

Interop_report/deploy.sh

+#!/bin/bash
+
+# This script is executed on the virtual machine during the *Deployment* phase.
+# It is used to apply parameters specific to the current deployment.
+# It is executed secondly during a cloud deployement in IFB-Biosphere, after the *Installation* phase.
+if [ $# -lt 1 ]
+then
+    APP_IMG="mbbteam/interop_report:latest"  
+else 
+    IMG_SRC=$1
+    case $IMG_SRC in
+        ifb)
+            APP_IMG="gitlab-registry.in2p3.fr/ifb-biosphere/apps/interop_report:master" ;;
+        docker )
+            APP_IMG="mbbteam/interop_report:latest"  ;;
+        local)
+            docker build . -t interop_report:latest 
+            APP_IMG="interop_report:latest" ;;
+        mbb)    
+            #APP_IMG="X.X.X.X:5000/interop_report:latest" ;;
+    esac
+fi
+
+
+# Tuning if site proxy or not
+#CLOUD_SERVICE = $(ss-get cloudservice)
+#CLOUD_SERVICE="ifb-genouest-genostack"
+
+#HOST_NAME=$( ss-get --timeout=3 hostname )
+HOST_NAME="192.168.100.49"
+#if [ "$CLOUD_SERVICE" == "ifb-genouest-genostack" ]; then
+    # Cloud site WITH a site proxy
+#    APP_PORT=80
+#    PROXIED_IP=$( echo $HOST_NAME | sed "s|\.|-|g")
+#    HOST_NAME="openstack-${PROXIED_IP}.genouest.org"
+#    HTTP_ENDP="https://$HOST_NAME"
+
+#    systemctl stop nginx
+#else
+    # Cloud site WOUT a site proxy
+    APP_PORT=8787
+    HTTP_ENDP="https://$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=AURA/L=Lyon/O=IFB/OU=IFB-biosphere/CN=myrstudio.biosphere.france-bioinformatique.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
+#fi
+
+# Docker volumes
+
+# mydatalocal: from the system disk or ephemeral  one
+IFB_DATADIR="/ifb/data/"
+source /etc/profile.d/ifb.sh
+VOL_NAME="mydatalocal"
+VOL_DEV=$(readlink -f -n $IFB_DATADIR/$VOL_NAME )
+DOCK_VOL=" --mount type=bind,src=$VOL_DEV,dst=$IFB_DATADIR/$VOL_NAME"
+
+# MBB Workflows reads data from /Data and write results to /Results
+mkdir ${VOL_DEV}/Data
+mkdir ${VOL_DEV}/Results
+DOCK_VOL+=" --mount type=bind,src=$VOL_DEV/Data,dst=/Data"
+DOCK_VOL+=" --mount type=bind,src=$VOL_DEV/Results,dst=/Results"
+
+# NFS mounts: from ifb_share configuration in autofs
+IFS_ORI=$IFS
+while IFS=" :" read VOL_NAME VOL_TYPE VOL_IP VOL_DEV ; do
+        DOCK_VOL+=" --mount type=volume,volume-driver=local,volume-opt=type=nfs,src=$VOL_NAME,dst=$IFB_DATADIR/$VOL_NAME,volume-opt=device=:$VOL_DEV,volume-opt=o=addr=$VOL_IP"
+done < /etc/auto.ifb_share
+IFS=$IFS_ORI
+
+
+
+CONTAINER_ID=$( docker run -d -p $APP_PORT:3838 $DOCK_VOL $APP_IMG )
+
+VM_IP=$(curl bot.whatismyipaddress.com)
+
+if [ $CONTAINER_ID ]
+then
+    echo " "
+    echo You have to put your Data on  : ${VOL_DEV}/Data
+    echo " "
+    echo Results will be written to    : ${VOL_DEV}/Results
+    echo " "
+    echo You can access the workflow interface at :  https://${VM_IP}
+    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
\ No newline at end of file

Interop_report/deployBigMem.sh

+#!/bin/bash
+#This script will help a deployment of a docker image on an MBB bigmem machine
+if [ $# -lt 1 ]
+then
+    APP_IMG="mbbteam/interop_report:latest"  
+else 
+    IMG_SRC=$1
+    case $IMG_SRC in
+        docker )
+            APP_IMG="mbbteam/interop_report:latest"  ;;
+        local)
+            docker build . -t interop_report:latest 
+            APP_IMG="interop_report:latest" ;;
+        mbb)    
+            #APP_IMG="X.X.X.X:5000/interop_report:latest" ;;
+    esac
+fi
+
+#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 $APP_PORT) != "" ]]
+then
+  echo "No tcp port available !!"
+  exit -1
+fi
+
+# Docker volumes
+#realUSER=$(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=$VOL_DEV/Results,dst=/Results"
+
+
+CONTAINER_ID=$( 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 " "
+    echo Results will be written to    : ${VOL_DEV}/Results
+    echo " "
+    hostname -I | awk -v port=$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
\ No newline at end of file

Interop_report/files/singularity.def

@@ -5,8 +5,9 @@ From: ../base.sif
 	export PATH=/opt/biotools/bin:$PATH
 	export ROOTSYS=/opt/biotools/root
 	export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:$ROOTSYS/lib'
-	
-
+	export LANG=en_US.UTF-8
+export LANGUAGE=en_US:en
+export LC_ALL=en_US.UTF-8
 
 %labels
 	Author YourName
@@ -89,3 +90,14 @@ singularity run --app appName this_container.sif
 
 	apt install -y gnuplot
 
+mkdir -p /share/apps/bin
+mkdir /share/apps/lib
+mkdir /share/apps/gridengine
+mkdir /share/bio
+mkdir -p /opt/gridengine
+mkdir -p /export/scrach
+mkdir -p /usr/lib64
+ln -s /bin/bash /bin/mbb_bash   
+ln -s /bin/bash /bin/isem_bash
+/usr/sbin/groupadd --system --gid 400 sge
+/usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
\ No newline at end of file

Interop_report/install.sh

+##### nginx install #####
+sudo apt-get install -y nginx
\ No newline at end of file

Interop_report/waw_workflow.qsub

+#!/bin/bash 
+#$ -S /bin/bash 
+# Job name 
+#$ -N WAW_worflow 
+# Using current working directory (otherwise, you will have to use '#$ wd /path/to/run') 
+#$ -cwd 
+# job time limits (h_rt is required [s_rt == software time limit / h_rt == hardware time limit]) 
+#$ -l h_rt=48:00:00 
+# Redirects the standard output to the named file. 
+#$ -o Results/waw.out 
+#$ -e Results/waw.err 
+module load singularity-3.1 
+
+dataDir=$1
+resultsDir=$2
+# Config file in a location binded to /Data or /Results 
+#ex. file in /home/khalid/dataanalyse/config.yaml
+#/home/khalid/dataanalyse/ is dataDir thet will be binded to /Data in the container
+#configfile must be set to /Data/config.yaml
+configFile=$3 
+cores=$4
+#if we must build the image from docker image
+singularity build interop_report.simg docker://mbbteam/interop_report:latest
+
+
+#Run the workflow in cmd line
+singularity exec -B $dataDir:/Data -B $resultsDir:/Results interop_report.simg snakemake  -s /workflow/Snakefile --configfile $configFile --cores $cores

Long_Read_Assembly/Dockerfile

@@ -57,5 +57,19 @@ RUN cd /opt/biotools \
  && cd quast-5.0.2/ \
  && python3 ./setup.py install_full
 
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US:en
+ENV LC_ALL en_US.UTF-8RUN mkdir -p /share/apps/bin  
+&& mkdir /share/apps/lib  
+&& mkdir /share/apps/gridengine  
+&& mkdir /share/bio  
+&& mkdir -p /opt/gridengine  
+&& mkdir -p /export/scrach  
+&& mkdir -p /usr/lib64  
+&& ln -s /bin/bash /bin/mbb_bash     
+&& ln -s /bin/bash /bin/isem_bash  
+&& /usr/sbin/groupadd --system --gid 400 sge  
+&& /usr/sbin/useradd --system --uid 400 --gid 400 -c GridEngine --shell /bin/true --home /opt/gridengine sge
+
 EXPOSE 3838
 CMD ["Rscript", "-e", "setwd('/sagApp/'); shiny::runApp('/sagApp/app.R',port=3838 , host='0.0.0.0')"]

Long_Read_Assembly/deploy.sh

+#!/bin/bash
+
+# This script is executed on the virtual machine during the *Deployment* phase.
+# It is used to apply parameters specific to the current deployment.
+# It is executed secondly during a cloud deployement in IFB-Biosphere, after the *Installation* phase.
+if [ $# -lt 1 ]
+then
+    APP_IMG="mbbteam/long_read_assembly:latest"  
+else 
+    IMG_SRC=$1
+    case $IMG_SRC in
+        ifb)
+            APP_IMG="gitlab-registry.in2p3.fr/ifb-biosphere/apps/long_read_assembly:master" ;;
+        docker )
+            APP_IMG="mbbteam/long_read_assembly:latest"  ;;
+        local)
+            docker build . -t long_read_assembly:latest 
+            APP_IMG="long_read_assembly:latest" ;;
+        mbb)    
+            #APP_IMG="X.X.X.X:5000/long_read_assembly:latest" ;;
+    esac
+fi
+
+
+# Tuning if site proxy or not
+#CLOUD_SERVICE = $(ss-get cloudservice)
+#CLOUD_SERVICE="ifb-genouest-genostack"
+
+#HOST_NAME=$( ss-get --timeout=3 hostname )
+HOST_NAME="192.168.100.49"
+#if [ "$CLOUD_SERVICE" == "ifb-genouest-genostack" ]; then
+    # Cloud site WITH a site proxy
+#    APP_PORT=80
+#    PROXIED_IP=$( echo $HOST_NAME | sed "s|\.|-|g")
+#    HOST_NAME="openstack-${PROXIED_IP}.genouest.org"
+#    HTTP_ENDP="https://$HOST_NAME"
+
+#    systemctl stop nginx
+#else
+    # Cloud site WOUT a site proxy
+    APP_PORT=8787
+    HTTP_ENDP="https://$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=AURA/L=Lyon/O=IFB/OU=IFB-biosphere/CN=myrstudio.biosphere.france-bioinformatique.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
+#fi
+
+# Docker volumes
+
+# mydatalocal: from the system disk or ephemeral  one
+IFB_DATADIR="/ifb/data/"
+source /etc/profile.d/ifb.sh
+VOL_NAME="mydatalocal"