First true commit

README.md

 # radseqref
 
+After quality checking of restriction enzyme-based data, such as RAD-seq, the sequences are demultiplexed and mapped with bowtie or bwa to a ref. genome. 
+The resulting bam files are then analysed with gstacks and populations from the Stacks pipeline.
\ No newline at end of file

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/radseqref:latest"  
+else 
+    IMG_SRC=$1
+    case $IMG_SRC in
+        ifb)
+            APP_IMG="gitlab-registry.in2p3.fr/ifb-biosphere/apps/radseqref:master" ;;
+        docker )
+            APP_IMG="mbbteam/radseqref:latest"  ;;
+        local)
+            docker build . -t radseqref:latest 
+            APP_IMG="radseqref:latest" ;;
+        mbb)    
+            #APP_IMG="X.X.X.X:5000/radseqref: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

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/radseqref:latest"  
+else 
+    IMG_SRC=$1
+    case $IMG_SRC in
+        docker )
+            APP_IMG="mbbteam/radseqref:latest"  ;;
+        local)
+            docker build . -t radseqref:latest 
+            APP_IMG="radseqref:latest" ;;
+        mbb)    
+            #APP_IMG="X.X.X.X:5000/radseqref:latest" ;;
+    esac
+fi
+
+
+#nginx 
+
+    # HOST_NAME="192.168.100.49"
+
+    # HTTP_ENDP="https://$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 $APP_PORT) != "" ]]
+then
+  echo "No tcp port available !!"
+  exit -1
+fi
+
+# Docker volumes
+#realUSER=$(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

install.sh

+##### nginx install #####
+sudo apt-get install -y nginx

system/nginx_conf.d_10-rstudio.conf

+map $http_upgrade $connection_upgrade {
+  default upgrade;
+  ''      close;
+}
+server {
+listen 80;
+listen [::]:80;
+server_name example.com;
+return 301 https://$server_name$request_uri;
+}
+server {
+listen 443 ssl http2;
+listen [::]:443 ssl http2;
+include snippets/self-signed.conf;
+include snippets/ssl-params.conf;
+location / {
+proxy_pass http://127.0.0.1:8787;
+proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+proxy_set_header Host $host;
+proxy_http_version 1.1;
+proxy_set_header Upgrade $http_upgrade;
+proxy_set_header Connection $connection_upgrade;
+}
+}
+

system/nginx_nginx.conf

+user nginx;
+worker_processes auto;
+error_log /var/log/nginx/error.log;
+pid /run/nginx.pid;
+include /usr/share/nginx/modules/*.conf;
+events {
+worker_connections 1024;
+}
+http {
+log_format main '$remote_addr - $remote_user [$time_local] "$request" '
+'$status $body_bytes_sent "$http_referer" '
+'"$http_user_agent" "$http_x_forwarded_for"';
+access_log /var/log/nginx/access.log main;
+sendfile on;
+tcp_nopush on;
+tcp_nodelay on;
+keepalive_timeout 65;
+types_hash_max_size 2048;
+include /etc/nginx/mime.types;
+default_type application/octet-stream;
+# Load modular configuration files from the /etc/nginx/conf.d directory.
+# See http://nginx.org/en/docs/ngx_core_module.html#include
+# for more information.
+include /etc/nginx/conf.d/*.conf;
+client_max_body_size 0;
+}
+

system/nginx_sites-available_default

+server {
+    listen 80 default_server;
+    listen [::]:80 default_server;
+    server_name server_domain_or_IP;
+    return 301 https://$server_name$request_uri;
+}
+
+server {
+
+    # SSL configuration
+
+    listen 443 ssl http2 default_server;
+    listen [::]:443 ssl http2 default_server;
+    include snippets/self-signed.conf;
+    include snippets/ssl-params.conf;
+    root /var/www/html;
+
+    # Add index.php to the list if you are using PHP
+    index index.html index.htm index.nginx-debian.html;
+
+    server_name _;
+
+    location / {
+            # First attempt to serve request as file, then
+            # as directory, then fall back to displaying a 404.
+            try_files $uri $uri/ =404;
+    }
+}
+

system/nginx_snippets_ssl-params.conf

+ssl_protocols TLSv1 TLSv1.1 TLSv1.2;
+ssl_prefer_server_ciphers on;
+ssl_ciphers "EECDH+AESGCM:EDH+AESGCM:AES256+EECDH:AES256+EDH";
+ssl_ecdh_curve secp384r1;
+ssl_session_cache shared:SSL:10m;
+ssl_session_tickets off;
+ssl_stapling on;
+ssl_stapling_verify on;
+resolver 8.8.8.8 8.8.4.4 valid=300s;
+resolver_timeout 5s;
+# Disable preloading HSTS for now.  You can use the commented out header line that includes
+# the "preload" directive if you understand the implications.
+#add_header Strict-Transport-Security "max-age=63072000; includeSubdomains; preload";
+add_header Strict-Transport-Security "max-age=63072000; includeSubdomains";
+# add_header X-Frame-Options DENY;
+add_header X-Content-Type-Options nosniff;
+
+ssl_dhparam /etc/ssl/certs/dhparam.pem;
+

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  radseqref.simg docker://mbbteam/radseqref:latest
+
+
+#Run the workflow in cmd line
+singularity exec -B $dataDir:/Data -B $resultsDir:/Results radseqref.simg snakemake  -s /workflow/Snakefile --configfile $configFile --cores $cores
\ No newline at end of file