On this page, useful info is gathered for the usage of django.ugent.be.
- RAM: 64 GiB (max: 64 GiB) DDR3-1600 RDIMM
- CPU: Intel(R) Xeon(R) CPU E5-2630 0 @ 2.30GHz
- HDD: 6 TB (HD3), 547GB (HD1), 275G (HD2)
- OS: openSUSE LEAP 15.0
Info on recent server usage can be found on http://www.kennybogaert.eu/servers/.
There are 3 disk partitions:
1. HD1 contains the operating system and databases
2. HD2 only databases: such as nr: /media/HD2/
3. HD3 /home directories in /media/HD3/home/
First, connect to the UGent network via VPN connection or kabel.
*For Linux users:
Just login via your commandline:
Or when programs with a graphical user interface need to be loaded (Rstudio, CLC genomics, ..)
ssh -X email@example.com
Programs can be run by executing the command:
For a good text editor:
or for clc genomics workbench:
*For Linux users:
just via commandline
port 22 is open.
VIA SCP(commandline)Copying file to host:
scp /some/local/file.txt firstname.lastname@example.org:/some/remote/directory/
scp email@example.com:/some/remote/file /some/local/directory/
scp -r firstname.lastname@example.org:/some/local/directory/ /some/local/directory/
Virtual Network Computing (VNC) is a graphical desktop sharing system that to remotely control another computer. On Django a VNC session will start the KDE desktop as a graphic user interface. When you close your VNC viewer on your local desktop all programs will keep running on the server and your server session remains the same when you login the next day.
This is ideal for using program that run a graphic user interface such as UGENE, CLC genomics workbench or Geneious.
UGENE and CLC work for all users.
Please contact if you wish to use Geneious.
Please note that if one user doesn’t close Geneious after using it, nobody can use it due to limitations of the licence! In this case, launching it from ssh -X (or mobaxterm) is a better habbit.
vncserver :an_available_vnc_number or vncserver
vncserver -geometry 1600x1200 :an_available_vnc_number
django.ugent.be:yourvncnumberencryption: Let VNC choose
vncserver -kill :an_available_vnc_number
ps -ef | grep "vnc"
init 3 init 5 && exit
Hard drive usage:
The main hard drive is very small. Therefore it can not be used for data storage. Please don’t leave intermediary files on the server and always keep track of the free disk space (using the kde widget, the df command, …). The server may run out of free space. This results in scripts terminating with an error, and makes the server unusable for programs demanding a lot of temporary storage.
IMPORTANT: Each months, you should receive an automatic email listing all files that are older than 3 months and got categorized as expired. In case there is no other option to clear space and ensure a working server, a script will be run that permanently deletes these expired files… Therefore don’t rely on the server for data storage!
This means we have an extra 6TB. This will alleviate the pressure on the primary partition and will make simultaneous analyses on large datasets more feasible again.
RAM & CPU usage
NCBI – nr database
blastx -query seq.fasta -db /home/nr/nr -out output.xml -outfmt 5
List of installed programs
blastall (legacy blast)
CLC genomics workbench
FASTX toolkit (0.0.13)
Geneious (v8.1.7) (contact to activate the licence)
Lotus [version 1.38]
UGENE (v 1.31)
- usearch [version 5.2.236] as usearch
- usearch [version 6.1.544] as usearch61
- usearch [version 8.0.1623_i86] as usearch8
- usearch [version 8.1.1861_i86] as usearch81
Note: This list is incomplete
Extra notes for specific program and pipelines
CLC workbench Updates
add to $HOME/.bashrc the following line
Anytime you want to use QIIME after installation with Miniconda, you’ll need to reactivate your
qiime1 environment using this command:
source activate qiime2-2018.6
accessible in path /mnt/lotus_pipeline/ eg. :
perl lotus.pl -h