Use of the cluster is free-of-charge to approved labs. However, to protect the cluster from abuse and prevent issues with storage, we have a few rules all users must follow. Failure to adhere to these rules will result in a warning. Additional rule violations will result in suspension of your account. Here are the rules:
- We will set-up your account and install any software you may need. Please do not install software yourself.
- In addition to your home account with is present at
/home/usernameon the server, you will also be given a data folder that is located on
/data/username. All data must be stored in this directory not your
- Data storage space is limited (10Tb goes quickly!), so we periodically montior storage space and may request that data not currently in use be moved off the cluster.
- We require a strong password for each account. We will set this password for you, and ask that you do not change it.
Configuring a new user (CHMI only)
sudo adduser [username] #adds a new user to the home directory usermod -aG sudo username #gives the new user sudo priveledges
Give the user access to all software on the server
/home/shared/softwares/and open the text file called
shared_software_list. This contains paths to all software. We routinely update this, so be sure to check back for new software paths:
- copy the contents of this file (highlight all, right-click, choose copy)
- open the terminal, and type
- scroll to the bottom of this file in the terminal and paste the paths under the last line
- hit ‘control x’ to exit nano. You’ll be asked if you want to save changes – select ‘y’ to save, then hit enter to finalize changes and close nano.
- for these changes to take effect, close the terminal, log out and then back in.
- you should now have access to all the software listed below
Connecting to the server
ssh firstname.lastname@example.org #you'll be prompted to enter your password and then you'll be connected #once connected you'll see a new prompt with username@ubuntu1604
|software||category||how to run|
|mothur||16S marker gene||
|QIIME2||16S marker gene||
|Cytoscape||network analysis||navigate to /home/shared/softwares/Cytoscape_v3.5.1 folder. Double click to open program|
|kallisto||mapping reads to transcripts||
|rsem||mapping reads to transcripts||
|Trinity||de novo transcriptome assembly||
|Picard tools||handling HTS file formats||
|samtools||handling HTS file formats||
|seqtk||handling HTS file formats||
|deeptools||analysis of HTS data||
|bcftools||SNP/variant discovery and genotyping||
|genome analysis toolkit (gatk)||SNP/variant discovery and genotyping||
|blast||sequence search||option include