FSU - Biological Science

FSU Biology - Computer Support Facilities - Pauper Cluster

Pauper Nodes Hardware Specs:

Pauper - (pauper.bio.fsu.edu → 128.186.176.80) - 56 Cores - 1.2 TB RAM - GTX1080 CUDA
Pauper2 - (pauper2.bio.fsu.edu → 128.186.176.81) - 144 Cores - 768 GB RAM
Pauper3 - (pauper3.bio.fsu.edu → 128.186.176.76) - 24 Cores - 256 GB RAM - GT760 CUDA
Pauper4 - (pauper4.bio.fsu.edu → 128.186.177.196) - 48 Cores - 768 GB RAM - RTX3050 CUDA
Pauper5 - (pauper5.bio.fsu.edu → 128.186.177.197) - 12 Cores - 128 GB RAM
Pauper6 - (pauper6.bio.fsu.edu → 128.186.177.198) - 12 Cores - 95 GB RAM
Data storage - 250 TB General use storage, 112 TB Private storage

Database, Library Mounts:

All pauper nodes - /home/alphafold2 (AlphaFold 2)
pauper.bio.fsu.edu - /alphafold (AlphaFold Protein Structure Database)
pauper2.bio.fsu.edu - /blast/blastdb (NIH Blast Database)

Pauper Nodes Installed Software:

INSTALLED FROM REPOSITORIES:

augustus
automake
bcftools
bedtools
bioperl
bioperl-run
blast2
bowtie
bowtie2
build-essential
bzip2
cd-hit
cmake
cowsay
cpp
curl
dialign
dos2unix
emacs
fastdnaml
fastp
fastqc
fasttree
file
firefox
flexbar
g++
gcc
gdebi
gdebi-core
git
gzip
hisat2
htop
imagej
jellyfish
kallisto
libcurl4-openssl-dev
libssl-dev
libvcflib-tools
libxml2-dev
mafft
make
minimap
minimap2
mpich
mrbayes
mysql-server
net-tools
nfs-common
nginx
njplot
openjdk-8-jdk
openjdk-11-jre
openssh-client
openssh-server
openssl
parallel
perl
python3-pip
primer3
pymol
python
r-base version 3: pauper, pauper2, pauper5, pauper6
r-base version 4: pauper3, pauper4
rasmol
raxml
samtools
screen
snp-sites
ssh
stringtie
tmux
trimmomatic
vcftools
vim

INSTALLED FROM SOURCE:

sratoolkit.2.9.6-ubuntu64
tabix-0.2.6
bedops_linux_x86_64-v2.4.39
bam-readcount
Geneious Prime
gffcompare
KAT

INSTALLED R PACKAGES:

openssl
credentials
httr
gert
gh
usethis
covr
xml2
roxygen2
rversions
devtools
conifur
gyro
converge
travis
genmat
genefilter
ballgown
BiocManager
edgeR
S4Vectors
GenomicRanges
rhdf5
biomaRt

NOT INSTALLED GLOBALLY, BUT USER CAN INSTALL IN /HOME:

miniconda :
Run "install_miniconda" and follow the prompts.
alphafold : Instructions. If you have installed miniconda all ready you can omit the first step.

MISC. SOFTWARE:

cuda (nvidia) - on Pauper & Pauper3
rstudio-server-1.4.1106-amd64 - on Pauper2

Instructions for connecting to the Pauper cluster:

Requesting Accounts

To request a Pauper account please submit a ticket to support-ticket@bio.fsu.edu or send an email to computer-support@bio.fsu.edu requesting an account. Please include your full name, FSUID and FSU email address in the ticket/email. Accounts are limited to FSU students, faculty and staff who are affiliated with the Biology department.

Requesting an invitation to the Pauper Cluster Email List Serve

To request an invitation to the Pauper cluster email list serve please submit a ticket to support-ticket@bio.fsu.edu or send an email to computer-support@bio.fsu.edu requesting an account. Please include your full name, FSUID and FSU email address in the ticket/email. Accounts are limited to FSU students, faculty and staff who are affiliated with the Biology department.

Software Install Scripts

For those who wish to build their own bioinformatics workstation identical to a pauper node the scripts we use to build our nodes are available here. These have been tested on Ubuntu 20.04. Be sure to read the readme.txt file before using any of these scripts.