rkrug/scrip.md

## scrip.md

      
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    Update Installation

sudo apt-get update
sudo apt-get upgrade

basic tools

sudo apt-get install mc
sudo apt-get install zile

Install newest R version

http://cran.rstudio.com/bin/linux/ubuntu/
Preparations

# update indices
sudo apt update -qq
# install two helper packages we need
sudo apt install --no-install-recommends software-properties-common dirmngr
# add the signing key (by Michael Rutter) for these repos
# To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc 
# Fingerprint: 298A3A825C0D65DFD57CBB651716619E084DAB9
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

Install R

sudo apt install r-base

Install build tools to compile packages

https://www.osradar.com/install-development-build-tools-ubuntu-20-04/
sudo apt install build-essential

Install RStudio server

https://www.rstudio.com/products/rstudio/download-server/debian-ubuntu/
sudo apt-get install gdebi-core
wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2021.09.1-372-amd64.deb
sudo gdebi rstudio-server-2021.09.1-372-amd64.deb

Prepare and packages via apt and install some basic packages

add-apt-repository ppa:c2d4u.team/c2d4u4.0+
sudo apt install \
r-cran-tidyverse \
r-cran-devtools \
r-cran-r-cran-desolve \
r-cran-nonlineartseries \
r-cran-earlywarnings \
r-cran-rootsolve \
r-cran-here \
r-cran-patchwork \
r-cran-rcppparallel \
r-cran-rapiserialize \
r-cran-stringfish \
r-cran-qs \
r-cran-rmarkdown

Create Volume

https://docs.s3it.uzh.ch/cloud/user_guide/4_create_and_manage_volumes/
Create the volume or use an existing volume and attach it to the instance
format volume

This should ponly be done when using a new and emplty volume.
If it is done on an existing volume with data, all data will be deleted!
Identify volume by using
sudo lsblk

which returns for example
NAME    MAJ:MIN RM  SIZE RO TYPE MOUNTPOINT
loop0     7:0    0 55.5M  1 loop /snap/core18/2074
loop1     7:1    0 55.5M  1 loop /snap/core18/2253
loop2     7:2    0 61.9M  1 loop /snap/core20/1242
loop3     7:3    0 70.3M  1 loop /snap/lxd/21029
loop4     7:4    0 67.2M  1 loop /snap/lxd/21835
loop5     7:5    0 32.3M  1 loop /snap/snapd/12704
loop6     7:6    0 42.2M  1 loop /snap/snapd/14066
vda     252:0    0  100G  0 disk
├─vda1  252:1    0 99.9G  0 part /
├─vda14 252:14   0    4M  0 part
└─vda15 252:15   0  106M  0 part /boot/efi
vdb     252:16   0   50G  0 disk

In this example, the drive is /dev/vdb/ and format it by using the following command. Make sure that you select the right device as you can not undo this action!
 sudo mkfs.ext4 -L RStudio_home /dev/vdb

Now you can mount it by using e.g.
 sudo mount /dev/vdb /mnt

and unmount it by using
 sudo umount /mnt

Setup automatic mounting of attached Volume

It is recommended to mount it automatically upon booting as outlined at at https://docs.s3it.uzh.ch/how-to_articles/how_to_automatically_mount_a_volume_at_instance_startup/
Create a directory to which the volume should be mounted
sudo mkdir /home_rstudio
sudo touch /home_rstudio/NOT_MOUNTED

Make a backup of the file /etc/fstab
sudo cp /etc/fstab /etc/fstab.old

use
sudo lsblk -o NAME,FSTYPE,UUID,SIZE,LABEL

to obtain the UUID of the volume. It is for examplke:
NAME    FSTYPE   UUID                                  SIZE LABEL
loop0   squashfs                                      55.5M
loop1   squashfs                                      55.5M
loop2   squashfs                                      61.9M
loop3   squashfs                                      70.3M
loop4   squashfs                                      67.2M
loop6   squashfs                                      42.2M
loop7   squashfs                                      61.9M
loop8   squashfs                                      43.3M
vda                                                    100G
├─vda1  ext4     075e8855-1060-4726-990b-e30daf3adb1d 99.9G cloudimg-rootfs
├─vda14                                                  4M
└─vda15 vfat     941F-05CE                             106M UEFI
vdb     ext4     743b569b-e81f-4618-ad79-86f59c80ffda  700G RStudio_home

The UUID is now 743b569b-e81f-4618-ad79-86f59c80ffda.
Now put the fiollowing line at the end of the file /etc/fstab` by using any editor you prefer ( nano is pre-installed and probably the easiest):
UUID=<UUID> /home_rstudio ext4 rw,user,noauto,x-systemd.automount,x-systemd.idle-timeout=300 0 0

where you replace <UUID> with the uuid identified above.
Important: At the end of the line you have to press return, i.e. the last line of the file needs to be an empty line!
Create snapshot of the instance

Now you are all set and should create a snapshot of the image.
Install SAMBA server and share home directories

TODO
See https://ubuntu.com/tutorials/install-and-configure-samba#2-installing-samba
sudo apt install samba

and setup samba to share all user directories by following this manual at https://www.howtogeek.com/howto/ubuntu/share-ubuntu-home-directories-using-samba/
Add User

sudo useradd -m -d /home_rstudio/NAME NAME

sudo passwd NAME PASSWORD

sudo smbpasswd -a NAME