Thanks for everyone that helped with their useful answers.

with several month trying different distros I found that the Ubuntu 16.04 LTS is one of best choices. Setup was easy to me, it has great support and updates all of my software work fine and I can easily use wine to run some windows programs like RDP4. All Java, Python and Perl based programs works fine and also I there are some amazing software in software center of Ubuntu. I can install most my bioinformatic software in terminal with simple codes, but in must case they are not up to date, I prefer to install them manually.

I tried biolinux, it was amazing but with old version of Ubuntu, it makes some challenges in diver compatibility.

Final words, Ubuntu 16.04 LTS was nice, easy to use, powerful and compatible with my needs in bioinformatics.

Thanks again to every one who helped me.

I found the switch between Windows to Ubuntu smooth. As far as I know, this is the most used distro at the moment and easiest to get help for.

between Fedora and Ubuntu (or OpenSuse) I recommend Ubuntu. Ubuntu has the largest community and largest programs. Maybe try LinuxMint, it is operating system based on ubuntu, easier for beginners and very stable. https://linuxmint.com/ 

You can use whatever you want, but Ubuntu and Linux Mint (an Ubuntu based distro) are the best choice not only for a begginer. I use Linux Mint and my coworkers use Ubuntu. There are also many blogs where you can find solutions for many problems you could have in many cases.

You can also the Linux Bash Shell on Windows 10, and use Ubuntu 16.04 by terminal.

https://www.ubuntu.com/

https://linuxmint.com/

https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/

I agree on Linux Mint 100% I use it for games and stuff on my home PC for 3 years works great, my mac dual boots to Mint 18.2. I don't recommend using windows at all unless absolutely necessary. I have not used any windows since 2007 and I am happy with my System 76 laptop and my Mac running Linux Mint.

I rather use Ubuntu than Mint, just because of the community it has. There is absolutely no problem that you can't find a solution for it in the community.

You could try Bio-Linux (http://environmentalomics.org/bio-linux/) it is Ubuntu based distro that contains most popular bioinformatics tools/packages

Ubuntu or Xubuntu work fine for most applications. Alot of tools have to be installed though, but i've found most of them in the APT pakage manager.

Hello Musa,

First, keep in mind that there is little difference between Debian, Ubuntu and Linux Mint.

Linux Mint is based on Ubuntu, and Ubuntu is based on Debian.

In fact, Linux Mint download packages straight from the Ubuntu servers.

The only difference between Ubuntu and Linux Mint is what software are installed by default, and how the user interface looks.

If you have never used GNU/Linux before, I recommend you to try Linux Mint XFCE.

XFCE is a very light desktop environment and it is configured correctly on Linux Mint.

If you need a specific biology software that is available for Ubuntu, then it's 100% compatible with Linux Mint.

Bio-Linux looks like a good idea, but the last release is nearly 4 years old. It might not suit you if you need the latest updates from your favourite software. As I said, all software pre-installed on Bio-Linux are already available on Ubuntu and Linux Mint, since Bio-Linux is based on Ubuntu.

And if, some day, you want to dive deeper into GNU/Linux, I recommend you to take a look at ArchLinux. It's a very different distribution suited only for advanced users.

As for Fedora, OpenSuse, Red Hat and CentOS, I've never used them long enough to have a clear opinion about them.

Hope that helps!

Best regards.

Thanks for everyone that helped with their useful answers.

with several month trying different distros I found that the Ubuntu 16.04 LTS is one of best choices. Setup was easy to me, it has great support and updates all of my software work fine and I can easily use wine to run some windows programs like RDP4. All Java, Python and Perl based programs works fine and also I there are some amazing software in software center of Ubuntu. I can install most my bioinformatic software in terminal with simple codes, but in must case they are not up to date, I prefer to install them manually.

I tried biolinux, it was amazing but with old version of Ubuntu, it makes some challenges in diver compatibility.

Final words, Ubuntu 16.04 LTS was nice, easy to use, powerful and compatible with my needs in bioinformatics.

Thanks again to every one who helped me.

Thanks Musa for the concluding remarks and sharing the experience.

I favor Xubuntu, currently version 16.04.

Managing doesn't cost you alot of your time. Prebuild packages from most programming languages are easy to install.

Some of my colleages use MINT, frankly i don't see much difference. It's more of a personal preference.

Xubuntu has the xface window manager which i had fewer problems with than using gnome.

You can always try a live CD, maybe the other window manager will suit you more.

Now that a few months have passed, are you still using Ubuntu? Are you planning to upgrade to Ubuntu 18?

The latest Bio Linux Ver. 8 I think is based on Ubuntu 14.04 LTS from 2014 (Ubuntu 14.04 is supported only until 2019 April) , Ubuntu 18.04 LTS is out (LTS means long term support in 18.04 case it will have support until 2023 April, and has longer support the regular Ubuntu that has 6-9 months support). the galaxy project that is main part of bio linux is available and can be installed on most Ubuntu and other ubuntu based distributions like Linux Mint, Ubuntu Mate, including Ubuntu 18.04. Ubuntu version 18.04 means released 2018 April, 14.04, 2014 April etc.

Aleksander, which one do you have? And do you know of any package dependencies issues when using 18.04?

Try on Galaxy 18.01 version. I am using custom build OS called AtlantisOS using BSD kernel, public linux distro name OriginOS using Linux Kernel. Since my custom LinuxOS uses same package installer like Ubuntu apt 99% sure will work on Ubuntu. Galaxy apt get install. From what I remember about Ubuntu if you use terminal to install apt solves all dependencies on its own. I will try next few days to install it on fresh new Ubuntu ans post install instructions here.

Test is done on Version Ubuntu 18.04 LTS downloaded from

https://www.ubuntu.com/download (May 1-th 2018), and it works.

How to install Galaxy (from Bio Linux on Ubuntu 18.04 LTS), from terminal or command line, just copy paste following command without "$".

for new install:

$ sudo apt-get update && apt-get upgrade

$ sudo apt-get install ssh git python

$ git clone -b release_18.01 https://github.com/galaxyproject/galaxy.git

$ cd galaxy

$ ./run.sh

for upgrade:

$ sudo apt-get update && apt-get upgrade

$ sudo apt-get install ssh git python

$ git fetch origin && git checkout release_18.01 && git pull --ff-only origin release_18.01

$ cd galaxy

$ ./run.sh

For Development version:

$ sudo apt-get update && apt-get upgrade

$ sudo apt-get install ssh git python

$ git clone https://github.com/galaxyproject/galaxy.git

$ cd galaxy

$ ./run.sh

=======================

installation takes 10-15 min or more depending on hardware and internet speed.

If you dont want to create config file use default, do this in terminal or command line, just copy paste following command without "$".

$ cp config/galaxy.yml.sample config/galaxy.yml

=======================

to access galaxy web based version write this is browser:

http://127.0.0.1:8080

or

http://localhost:8080

or

replace 127.0.0.1 with IP address of server you install it on.

=======================

more details available on the community page https://galaxyproject.org/

I'm using Ubuntu 18.04 as dual boot with ubuntu 16.04. We have to test most of packages. At this point ubuntu 16.04 is best version of ubuntu (because of its great community support), also ubuntu 18.04 works fine but it is much better to for point release (18.04.1). Maybe it is better to use both until testing all aspects of ubuntu 18.04.

You have to test both bioinformatic softwares and all general softwares, like drivers.

I was straggling for two days to install ubuntu 18.04. Finally I found that it was all about nvidia graphic driver. There was no help for this problem in ubuntu 18.04, also helps and comments for ubuntu 16.04 was not usefull. But after installation there was no problem. I tesed phylogenetic packages and java based programs but there was no time to check R based packages.

using only intel gpu, cpu and motherboard so never had problems with linux or bsd with it, intel works out of the box always with open source.

I installed r r-base and r-base-dev and r studio on 18.04 and it works.

Musa if you use 16.04 LTS version, it has support until 2021 April so if that works for you if you ask me no need to upgrade if you don't have to.

R and R Studio can be installed on 14.04 Ubuntu from 2012, downside of it is that it has support only until 2019 April.

I’ve installed 18.04 and everything works. I set up as dual boot with windows. I had to change some settings in BIOS and update the firmware ahead of installation. I had no problem installing R and R studio. I can let you know about the rest one I have a bit more experience. I am setting up galaxy now.

Lourdes Acosta if I can get more info about all the names of the packages or applications used in bio linux it would help me a lot, I have few colleagues that use bio linux for work, I prefer they use Ubuntu 18.04. Thank you in advance.

OK. I will have a look and post back.

The list of packages is here: http://environmentalomics.org/bio-linux-software-list/

thank you very much Lourdes

CentOS and opensuse is good and highly stable.

Ubuntu 16.04 LTS, on Oracle VirtualBox (no reboot required). Soon 18.04. Host: Windows 10.

Never had problems finding current packages in Ubuntu.

Hi,

I would just say:

East or West,

Ubuntu is the Best!

Regards

I just got an Alienware computer with Windows 10. I would like to remove it and install Ubuntu 16 or 18, but I am a bit afraid of facing nvidia card dirver problems. Musa Mohammadi you mentioned you had some issues with the nvidia graphic driver when installing ubuntu 18.04. What kind of problems? How did you solve them? I still can't decide if I keep dual booting for windows and Ubuntu or only Ubuntu. Anyone else has experience with Alienware and ubuntu?

Eugenia Zarza try linuxmint 18 is based on ubuntu 18.04 19 is based on ubuntu 18.10 the driver support is excellent, start driver apps and install, I have been using Linux Mint for many years, everything Nvidia and Intel works 99%. I would not recommend dual boot if you need windows use VirtualBox (virtual machine) especially with Windows 10. If you need any advice feel free to message me about Linux.

It depends on how many experience you have using linux, I rather practicing on biolinux or other Ubuntu-based distro, because they are friendlier than others and dont have many hardware issues. If you have a low resources computer, you can try with Xubuntu or Lubuntu and install bioinformatic software. Another option is Manjaro or Antergos but Arch distros can fail with some updates and hardware drivers, but they are the fastest ones.

I have used to work with Bio-linux and it´s perfectly working... All the best :)

Thanks for your answers. I ran into some hardware specific problems to install linux. Something related to this: https://www.dell.com/community/Alienware-General-Read-Only/Aurora-R6-selected-boot-device-failed/td-p/5608394.

So I activated the Windows Subsystem for Linux with Ubuntu 16. I installed and ran the QIIME2 pipeline and is working fine. I think this could be a good alternative for people that cannot dual boot or replace windows entirely.

This is a very informative discussion. Thank you for bringing it up, Musa. Am using Biolinux, but looking forward to trying out linuxmint.