Re install script

This script is used to install bioinformatics software and it's required libraries on a clean linux (ubuntu-like) install.

This means that libraries can be installed with apt-get.

I update this git when new versions of software have appeared. For my work desktop computer I'll run the full script Concerning other computers I'll just execute some lines. This git is a MEMO for myself. You are welcome to make corrections and suggestions.

Use under your own risk.

Managing users in command line

There are some legacy commands, they start with user-, they are still used but are less versatile. https://askubuntu.com/questions/345974/what-is-the-difference-between-adduser-and-useradd

Add user

Use adduser not useradd. The first one is a perl overlay with extra options making the process easier:

First create a new user, then you can add it to different groups withouth changing its main group:

sudo adduser user
sudo usermod -aG sudo user

Details about adding users/groups:

--system creates accounts which do not have a password and thus one cannot log in with them. They are used for services
The default group when adding a user is his own user group
The list of all users can be found here: /etc/passwd
The configuration of for new users is defined in /etc/adduser.conf
All the files in /etc/skel/ will be copied to the new user's home

Choose groups

There are some default groups for users and for admin/sudo users, The most common groups for admin are: adm, cdrom, lpadmin, sudo, sambashare, dip, plugdev

adm and sudo are equivalent groups. adm seems to be a legacy group that is now covered by sudo but it still exists and is being used as default in ubuntu.

For more details: https://askubuntu.com/questions/219083/default-groups-for-user-in-ubuntu

Change main group for a user:

To change the main group and keep the secondary groups use the -G parameter with the list of secondary groups. Here's an example of the groups

sudo usermod -g PrimaryGroup -G user,sudo,adm,sambashare,lpadmin user

Default

Remove users

To remove a user and remove all directories with its name use -r It will remove the mail spool as well as its home directory.

userdel -r

Adding disks

To add a new disk it needs to be:

Find the device : https://linuxhandbook.com/linux-list-disks/
Create a partition table (Go with GPT, its newer and manages volumes larger than 2Tb)
Format it: https://linuxhandbook.com/mkfs-command/
Mount it
Manage permissions and add project directories
(Optionnal) Add it ti /etc/fstab if you want the disk to be mounted at start-up: https://askubuntu.com/questions/303497/adding-an-entry-to-fstab

How to chose a format ?

Will this drive go with Windows and Linux → NTFS (ou exFAT for usb devices). No contact with windows → ext4

NTFS and ext4 are both journaled partition systems.

Same with the code

## Find the volumes
sudo fdisk -l
## These are other options: df, lsblk, blkid, cfdisk, parted, sfdisk

## Create a partition table, follow the guide, in the help or the link in the previous paragraph
## example given with /dev/sdb.
## Use 'g' for GPT,
## 'n' for a new partition (keep defaults for 1 only partition)
## 'p' to print choices
## 'w' to write the choices
## 'm' to get the menu of all commands within fdisk.
fdisk /dev/sdb

## Format it to ext4
sudo mkfs.ext4 -F /dev/sdb1

## Mount it on a directory
sudo mkdir -p /mnt/volume_name
sudo mount /dev/sdb1  /mnt/volume_name/

R-cran stuff

Installing R goes pretty smoothly using the instructions from the CRAN. Some networks at work would block you from downloading the latest version of R-core. You have to add a port and some extra letters to the command, it is listed in installs.sh.

To be tested: Else you can install R via conda. This allows to install a different set of R environments. This may also help avoid the conflict of updating R-core packages while using BioConductor.

If you want R to quit smoothly without asking to save the RData and session, you can follow the instructions on this link: https://stackoverflow.com/questions/4996090/how-to-disable-save-workspace-image-prompt-in-r/4996252#4996252 Else you can get the .Rprofile file in this same repository.

Installing conda

Maybe in the future moving to pixi will be a good idea. As of today, pixi has not integrated snakemake.

Prefere lighter installers (most to least advised): miniforge < miniconda < anaconda

Check the configuration of the channels:

conda list
conda list export --explicit > environment.yml

Remove the default channels and the anaconda channels that might not be open/free anymore. Set the most convenient channels

conda config --remove channels defaults
conda config --remove channels anaconda
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

3nrique0/re-install_script