CHMI maintains a custom configured compute server that runs Linux Ubuntu 16.04 LTS. This machine has two 6-core Intel Xeon E5-2643v4 CPUs (12 cores total), 512 Gb of RAM and 10Tb of RAID1 storage. If you are a PennVet lab and wish to use this machine, please contact Dan Beiting ( for more information.
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General rules

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/username on 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 home/username folder.
  • 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

  • navigate to /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 nano .profile.
  • 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 username@
#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

Available software

software category how to run
mothur 16S marker gene mothur
QIIME2 16S marker gene source activate /home/beiting/anaconda3/envs/qiime2-2017.10
Sunbeam metagenomics source activate sunbeam
MetaPhlAn metagenomics
GraPhlAn metagenomics, visualization
anvi’o metagenomics, visualization source activate /home/beiting/anaconda3/envs/anvio3
Circos general visualization circos
Cytoscape network analysis navigate to /home/shared/softwares/Cytoscape_v3.5.1 folder. Double click to open program
bowtie2 sequence alignment bowtie2
bwa sequence alignment bwa
Star sequence alignment STAR (all caps)
kallisto mapping reads to transcripts kallisto
rsem mapping reads to transcripts rsem-(function)
Mash comparative genomics mash
Nextflow workflow management nextflow
Trinity de novo transcriptome assembly Chrysalis (uppercase ‘C’), inchworm
Picard tools handling HTS file formats picard
samtools handling HTS file formats samtools
seqtk handling HTS file formats seqtk
deeptools analysis of HTS data deeptools
bcftools SNP/variant discovery and genotyping bcftools
genome analysis toolkit (gatk) SNP/variant discovery and genotyping java -jar /home/shared/softwares/gatk-3.8-0/GenomeAnalysisTK.jar
blast sequence search option include blastn, blastp, pr blastx
clust co-expression modules clust