– we11sv01 user tips

On this page, useful info is gathered for the usage of we11sv01.ugent.be.

Server Specs

  • PowerEdge R430 Server
  • RAM: 320 GiB (max: 384 GiB) DDR4 2133 REG-DIMM
  • CPU: 12 cores – 24 threads (2x Intel Xeon E5-2620 v3 2.4GHz,15M Cache,8.00GT/s QPI,Turbo,HT,6C/12T (85W) Max Mem 1866MHz)
  • HDD: 18 TB
  • OS: Ubuntu 16.04 LTS (Xenial Xerus)

Info on recent server usage can be found on http://www.kennybogaert.eu/servers/.

Installed Software

Additional packages:

  • R version 3.4.4 (2018-03-15)
  • Rstudio v1.1453
  • amos v3.1.0
  • bowtie2 version 2.3.4
  • blat v. 36×2
  • cufflinks v2.2.1
  • diamond v0.9.14
  • kallisto v0.43.1
  • MaxBin v2.2.4
  • multiqc v1.7
  • picrust v1.1.3
  • salmon v0.12.0
  • samtools v1.7
  • spades v3.11
  • sratools 2.9.0 eg. fastq-dump.2.9.0
  • Stacks v2.4
  • Trinity-v2.8.4
  • usearch v8.1.1861_i86linux32
  • usearch v10.0.240_i86linux32
  • racon v1.2.0
  • unicycler v0.4.4

Optional manual environments (modify your $PATH):

  • MyCC (including cd-hit v4.6, fetchMG, Cython-0.22, scikit-learn-0.10.0, etc. see https://sourceforge.net/projects/sb2nhri/files/MyCC/)
export PATH="/opt/MyCC:/opt/MyCC/fetchMG:$PATH"

Conda environments (modify your $PATH):

add to $HOME/.bashrc the following line

export PATH="$PATH:/home/bioadmin/miniconda3/bin"

note: do not change the order

  • prokka 1.13 (https://github.com/tseemann/prokka)
source activate base 
  • picrust v1.1.3
conda activate picrust_env
  • QIIME2
source activate qiime2-2018.6
  • salmon v 0.12.0
source activate salmon

note:  To exit the environment, simply run the deactivate command:

source deactivate


For running trinity please download the recent trinity version locally in ~/bin

load salmon v.0.12.0 via conda

source activate salmon

And run Trinity in this environment.

Login SSH

First, connect to the UGent network via VPN connection or kabel.

*Linux users:

connect via ssh to django.ugent.be on linux:
ssh username@we11sv01.ugent.be

scripts can be run in the background using nohup

nohup command &
nohup command >/dev/null 2>&1 & # creates no nohup.out

Or when programs with a graphical user interface need to be loaded (Rstudio, CLC genomics, ..)

ssh -X username@we11sv01.ugent.be 

Optional (modify your path) :

*Windows users:

Windows users may install a free client as alternative. (https://mobaxterm.mobatek.net/)


A. Commandline (only UNIX):*


-Copying file to host:

scp /some/local/file.txt username@we11sv01.ugent.be:/some/remote/directory/
-Copying file from host to local directory:
scp username@we11sv01.ugent.be:/some/remote/file /some/local/directory/
-Copying directory from host
scp -r user@we11sv01.ugent.be:/some/local/directory/   /some/local/directory/


VIA FILEZILLA or other FTP client*
host: we11sv01.ugent.be
user: yourusername
password: youraccountpassword
port: 22
*Windows users can also install WinSCP (https://winscp.net/eng/download.php), a free FTP and SCP client.