geany fix

Docker-BioInf.sh

@@ -100,16 +100,20 @@ fi
 
   exit  # Not start later code automatically
   #run command for users
-  awk -F"\t" '!/^#/ {print $NF}' users.tsv | xargs -l1 bash -c 
-  awk -F"\t" '!/^#/ {print $NF}' staff.tsv | xargs -l1 bash -c 
+  cat  staff.tsv users.tsv | awk -F"\t" '!/^#/ {print $NF}' | xargs -l1 bash -c 
   # lazy unmount 
-  awk -F"\t" '!/^#/ {print $NF}' staff.tsv | sed 's/fusermount -u/fusermount -zu/g' | xargs -l1 bash -c 
+  cat  staff.tsv users.tsv | awk -F"\t" '!/^#/ {print $NF}' | sed 's/fusermount -u/fusermount -zu/g' | xargs -l1 bash -c 
   # unmount all
-  awk -F"\t" '!/^#/ {print $NF}' staff.tsv | sed 's/;.*/"/g' | xargs -l1 bash -c 
-  # reload NGINX in staff's dockers (to update Letsencrypt certificate)
-  awk '!/^#/ {print $2}' staff.tsv | xargs -i docker exec {} /usr/bin/supervisorctl -c /etc/supervisor/conf.d/supervisord.conf restart 6_nginx
+  cat  staff.tsv users.tsv | awk -F"\t" '!/^#/ {print $NF}' | sed 's/;.*/"/g' | xargs -l1 bash -c 
   # update staff's dockers
-  awk '!/^#/ {print $2}' staff.tsv | xargs -i docker exec {} /usr/bin/supervisorctl -c /etc/supervisor/conf.d/supervisord.conf start 7_update
+  cat  staff.tsv users.tsv | awk '!/^#/ {print $2}' | xargs -i docker exec {} /usr/bin/supervisorctl -c /etc/supervisor/conf.d/supervisord.conf start 7_update
+  cat  staff.tsv users.tsv | awk '!/^#/ {print $2}' | xargs -i docker exec {} env DEBIAN_FRONTEND=noninteractive /etc/supervisor/conf.d/update.sh 2>&1 | grep -E "/home/|upgraded|dpkg|amd64"
+  cat  staff.tsv users.tsv | awk '!/^#/ {print $2}' | xargs -i docker exec {} env DEBIAN_FRONTEND=noninteractive dpkg --configure --force-confold -a
+  cat  staff.tsv users.tsv | awk '!/^#/ {print $2}' | xargs -i docker exec {} env DEBIAN_FRONTEND=noninteractive apt --fix-broken install -y
+  cat  staff.tsv users.tsv | awk '!/^#/ {print $2}' | xargs -i docker exec {} env DEBIAN_FRONTEND=noninteractive apt install --no-install-recommends -y jupyter-notebook
+  # reload NGINX in staff's dockers (to update Letsencrypt certificate)
+  cat  staff.tsv users.tsv | awk '!/^#/ {print $2}' | xargs -i docker exec {} /usr/bin/supervisorctl -c /etc/supervisor/conf.d/supervisord.conf restart 6_nginx
+  cat  staff.tsv users.tsv | awk '!/^#/ {print $2}' | xargs -i docker exec {} /usr/bin/supervisorctl -c /etc/supervisor/conf.d/supervisord.conf restart 5_sshd
   # Check the mounted folders for staff
   mount | awk -F '/' '/\/home/ {print $4}' > mounted.lst && awk '!/^#/ {print $2}' staff.tsv > staff.lst && grep -vxf mounted.lst staff.lst > mount.lst 
   awk -F"\t" '!/^#/ {print $NF}' staff.tsv | grep -f mount.lst | xargs -l1 bash -c 
@@ -137,12 +141,14 @@ fi
 nuser="user300"
   echo $nuser
   docker top $nuser
+  docker logs $nuser
   docker restart $nuser
   awk -F"\t" "/\t$nuser\t/ {print \$NF}" staff.tsv | xargs -l1 bash -c
   docker exec $nuser /usr/bin/supervisorctl -c /etc/supervisor/conf.d/supervisord.conf restart 5_sshd
   docker exec $nuser /usr/bin/supervisorctl -c /etc/supervisor/conf.d/supervisord.conf restart 6_nginx
   docker exec $nuser /etc/supervisor/conf.d/update.sh
-  docker exec $nuser apt --fix-broken install -y
+  docker exec -it $nuser bash
+  docker exec $nuser env DEBIAN_FRONTEND=noninteractive apt --fix-broken install -y
   awk -F"\t" "/\t$nuser\t/ {print}" staff.tsv | tr '\t' ' ' | sudo xargs -l -P 10 ./Docker-BioInf-per-student.sh
   docker stop $nuser
   docker rm $nuser

Dockerfile

@@ -1,4 +1,5 @@
 FROM  debian:testing
+#  docker run -it -rm --name test debian:testing bash
 RUN sed -i 's/main$/main contrib non-free non-free-firmware/' /etc/apt/sources.list.d/debian.sources && \
   env DEBIAN_FRONTEND=noninteractive apt-get update --allow-releaseinfo-change && \
 	env DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends apt-utils whiptail && \
@@ -7,7 +8,7 @@ RUN sed -i 's/main$/main contrib non-free non-free-firmware/' /etc/apt/sources.l
 	env DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
 		locales sudo mc curl wget procps psmisc htop nginx-light libnginx-mod-http-auth-pam usrmerge \
 		shellinabox ssh mosh tmux supervisor bash-completion gpm bzip2 \
-		at-spi2-core policykit-1-gnome dbus-x11 firefox-esr gpicview zathura geany meld fonts-firacode \
+		at-spi2-core policykit-1-gnome dbus-x11 firefox-esr gpicview zathura meld fonts-firacode \
 		build-essential gfortran libgfortran-13-dev liblapack-dev libblas-dev libopenblas-dev \
 		libxml2-dev libjpeg-dev libcurl4-openssl-dev libssl-dev zlib1g-dev \
 		lxde-core lxlauncher lxterminal lxmenu-data lxtask synaptic xarchiver \
@@ -18,7 +19,7 @@ RUN sed -i 's/main$/main contrib non-free non-free-firmware/' /etc/apt/sources.l
 		sortmerna bcftools gnumeric bedtools gffread igv && \
 	apt-get autoremove -y && \
 	apt-get autoclean -y
-# GTK 2 and 3 settings for icons and style, wallpaper   # tophat fastx-toolkit 
+# GTK 2 and 3 settings for icons and style, wallpaper   # apt-get install -y --no-install-recommends tophat fastx-toolkit geany
 RUN echo 'gtk-theme-name="Raleigh"\ngtk-icon-theme-name="nuoveXT2"\n' > /etc/skel/.gtkrc-2.0 && \
 	mkdir -p /etc/skel/.config/gtk-3.0 && \
 	echo '[Settings]\ngtk-theme-name="Raleigh"\ngtk-icon-theme-name="nuoveXT2"\n' > /etc/skel/.config/gtk-3.0/settings.ini && \