IT-Services::Evop

Info and manual page regarding the IT setup (hard- and software) for the EVOP 2020 workshop


IT-Services::Evop - Login Server

The server provided for the workshop is called evop-login (FQDN: 'evop-login.imp.fu-berlin.de'). It is a VM with 16 cores and 128 GB RAM that runs Debian "Buster" Linux and has 3 TB local storage.

IT-Services::Evop - Fileserver - Backup/Protection

The following security/backup measures are in place and active:
  • RAID - protection in case of physical failure of single disks
  • Backup - nightly mirroring of the content of the /srv/ directory to a dedicated backup server

IT-Services::Evop - Desktop PCs

  • Apart friom the login server, there are 30 desktop PCs available in the workshop venue :
    • OS: Linux (Debian "Buster")
    • CPU: Intel i5 (9. Generation)
    • 32 GB RAM
    • Graphics: Intel chipset (onboard graphics)
    • local storage: 500 GB NVMe SSD (in each PC)
    • 27" TFT-Monitor for each PC
  • The desktop PCs are named
    • evop01.imp.fu-berlin.de
    • evop02.imp.fu-berlin.de
    • ...
    • evop30.imp.fu-berlin.de

IT-Services::Evop - Desktop-PCs - Backup

ALERT! There is no backup done for the 30 desktop PCs.

IT-Services::Evop - Network access to the Evop server + desktop PCs

Access from within the FU campus network

The server and the desktop PCs are accessible via SSH (remote login), but only from within the Freie Universität's campus network, not from the Internet.

Access from the Internet

From outside FU's campus net, you will have to use our departmental login node andorra.imp.fu-berlin.de as a "jump host". On 'andorra', you can SSH login with password from the Internet. From 'andorra', you can then connect via SSH to the evop server and clients (or, if you are very familiar with SSH, you can "tunnel" to the evop computers through 'andorra').

IT-Services::Evop - WiFi access

For mobile computers/devices brought by the participants, there are two possible ways to connect them to the Internet via WiFi network (wireless LAN, WLAN): For people coming from instituions that participate in the world-wide eduroam or who have been provided with an FU account for the workshop can use the eduroam wifi network. Besides, there will be a temporary wifi network conference available for the participants during the time of the workshop.

Alternative 1: WiFi access via eduroam network

Alternative 2: WiFi access via conference network

Connect to the WiFi network with the name (SSID) conference. You then need to enter an access key that is valid for 14 days (and hence needs to be changed once in the middle of the workshop)
  1. WLAN Key gültig / valid 24.02.-08.03.2020: ...
    (bitte beim Veranstalter erfragen! / please ask the workshop chairs! )
  2. WLAN Key gültig / valid 09.03.-22.03.2020: ...
    (bitte beim Veranstalter erfragen! / please ask the workshop chairs! ))

further details on using the conference WiFi can be found here:

IT-Services::Evop - HOME directories

The HOMEs will be computer-*local*, i.e. when you are logged in to the server, you have another home than on any of the desktop PCs, even though they have the same path /home/accountname/ on all computers (example: /home/k00319285/ for user account k00319285 ). Additionally, on the login server, we have created a "group folder" /opt/evop/public/ where you can deposit materials (documents, computation data) for the students. The /opt/evop/public/ directory is exported via NFS from the login server to the desktop PCs, so example data etc. that is stored there is also easily available on the 30 desktop PC (without any need to copy it).

IT-Services::Evop - IT support contact details

If you have any further questions or if you should encounter problems with the set-up, please direct all communication to the support e-mail address we have established for the EVOP workshop: evop-support@mi.fu-berlin.de .

IT-Services::Evop - Software

The login server and the desktop PCs are running Debian Linux "Buster" and provide the following biocomputing specific software environment:

Software packages manually installed

installed under /opt/evop/ (also available on the client PCs )

NameSorted ascending Version Homepage/Download
abctoolbox ? http://cmpg.unibe.ch/software/ABCtoolbox/
Admixture 1.3.0 http://software.genetics.ucla.edu/admixture/
anaconda 4.7.12 https://www.anaconda.com/download/#linux
anaconda Python 3   part of the anaconda installation
arlecore 3.5.2.2 http://cmpg.unibe.ch/software/arlequin35/Arl35Downloads.html
arlsumstats 29.07.2007 http://cmpg.unibe.ch/software/arlequin35/Arl35Downloads.html
ASTRAL 5.6.3 https://github.com/smirarab/ASTRAL
Bayescan 2.1 http://cmpg.unibe.ch/software/BayeScan/download.html
BMGE 1.12 ftp://ftp.pasteur.fr/pub/gensoft/projects/BMGE/
bokeh 1.3.4 https://bokeh.pydata.org/en/0.10.0/docs/userguide/notebook.html
Canu (Assembler) v1.9 https://github.com/marbl/canu
dadi 1.7.0 https://bitbucket.org/gutenkunstlab/dadi
Distruct 1.1 https://rosenberglab.stanford.edu/distruct.html
duk 03.03.2011 http://duk.sourceforge.net/
FastME 2.1.6.1 https://gite.lirmm.fr/atgc/FastME/
fastq-pair 0.3 https://github.com/linsalrob/fastq-pair
fastsimcoal26 2.6.0.2 http://cmpg.unibe.ch/software/fastsimcoal2/
fastStructure 1.0 https://github.com/rajanil/fastStructure
GATK 3.6
4.1.4.1
https://github.com/broadgsa/gatk/releases/tag/3.6
https://github.com/broadinstitute/gatk/releases
genscan ??? (old, < 2010) http://genes.mit.edu/GENSCAN.html
gethomologues 26022020 https://github.com/eead-csic-compbio/gethomologues
igvtools + IGV Genome browser 2.8.0 https://software.broadinstitute.org/software/igv/
ipyrad 0.9.43 https://ipyrad.readthedocs.io/en/latest/3-installation.html
IQTREE please install the latest version 1.6.12 http://www.iqtree.org/#download
jmodeltest2 2.1.10 https://github.com/ddarriba/jmodeltest2
maker 2.31.10 http://yandell.topaz.genetics.utah.edu/makerdownloads
megahit 1.2.9 https://github.com/voutcn/megahit
msmc2 2.1.1 https://github.com/stschiff/msmc2
MultiQC 1.0.dev0 https://multiqc.info/
mummer4 4.0.0beta2 https://github.com/mummer4/mummer
Orthofinder 2.3.11 http://www.stevekellylab.com/software/orthofinder
pear 0.9.11 pear-src-0.9.11.tar.gz
PGDSpider 2.1.1.5 http://www.cmpg.unibe.ch/software/PGDSpider/
Aufruf via Java Webstart: http://www.cmpg.unibe.ch/software/PGDSpider/jnlp/PGDSpider2.jnlp
PHYLOBAYES MPI 1.8 https://github.com/bayesiancook/pbmpi
(http://megasun.bch.umontreal.ca/People/lartillot/www/downloadmpi.html)
PREQUAL 1.02 https://github.com/simonwhelan/prequal
pyspark-notebook   https://hub.docker.com/r/jupyter/pyspark-notebook/
qiime2   https://qiime2.org/
Repeat Masker 4.0.7 http://www.repeatmasker.org/RMDownload.html
rnacount ? https://github.com/qbicsoftware/rnacount
rnacounter 1.5.2 https://pypi.org/project/rnacounter/
Stacks 2.5 http://catchenlab.life.illinois.edu/stacks/
Structure 2.3.4 https://web.stanford.edu/group/pritchardlab/structure.html
SweeD (Sweepfinder) 3.2.1 https://cme.h-its.org/exelixis/web/software/sweed/index.html
TreeMix 1.13 https://bitbucket.org/nygcresearch/treemix/wiki/Home
vega + vega-lite 2.6.0  
VEP 99.2 https://www.ensembl.org/info/docs/tools/vep/index.html

R packages installed (including BioConductor-Packages)

installed under /usr/lib/R/site-library/ or /usr/local/lib/R/site-library
(only available on the server evop-login . )

abind
acepack
ade4
adegenet
agricolae
AlgDesign
animation
annotate
AnnotationDbi
AnnotationFilter
AnnotationForge
ape
askpass
assertthat
backports
base64enc
base64url
BatchJobs
batchtools
bayesplot
BBmisc
BH
bindr
bindrcpp
Biobase
BiocGenerics
BiocInstaller
BiocManager
BiocParallel
BiocVersion
biomaRt
Biostrings
bit
bit64
bitops
blob
brew
broom
callr
caret
Category
caTools
cellranger
checkmate
chron
classInt
cli
cliapp
clipr
clisymbols
clusterGeneration
clusterProfiler
coda
CoDiNA
colorspace
colourpicker
combinat
commonmark
covr
cowplot
crayon
crosstalk
curl
CVST
data.table
DBI
DBItest
dbplyr
ddalpha
DelayedArray
deldir
DEoptimR
desc
DESeq2
devtools
dials
DiceDesign
digest
dimRed
DO.db
doMC
doParallel
DOSE
dplyr
DRR
DT
dygraphs
e1071
earth
edgeR
ellipsis
enrichplot
EnsDb.Hsapiens.v86
ensembldb
europepmc
evaluate
expm
fansi
farver
fastICA
fastmap
fastmatch
ff
fgsea
filehash
forcats
foreach
formatR
Formula
fs
furrr
futile.logger
futile.options
future
future.apply
gdata
gdsfmt
genefilter
geneplotter
genepop
generics
GenomeInfoDb
GenomeInfoDbData
GenomicAlignments
GenomicFeatures
GenomicRanges
geometry
getopt
GGally
ggforce
ggplot2
ggplotify
ggraph
ggrepel
ggridges
gh
git2r
globals
glue
gmodels
GO.db
GOSemSim
GOstats
gower
GPfit
gplots
graph
graphlayouts
gridExtra
gridGraphics
GSEABase
gtable
gtools
hardhat
haven
here
hexbin
highr
Hmisc
hms
htmlTable
htmltools
htmlwidgets
httpuv
httr
hunspell
hwriter
igraph
infer
ini
inline
ipred
IRanges
IRdisplay
IRkernel
isoband
ISOcodes
iterators
janeaustenr
jsonlite
kernlab
klaR
knitr
labeling
labelled
lambda.r
later
latticeExtra
lava
lazyeval
LearnBayes
lhs
lifecycle
limma
linprog
listenv
littler
lme4
locfit
loo
lpSolve
lubridate
magic
magick
magrittr
mapproj
maps
maptools
markdown
matrixStats
mda
memoise
mime
miniUI
minqa
mlbench
MLmetrics
mnormt
mockery
mockr
ModelMetrics
modelr
multicore
munsell
nloptr
numDeriv
openssl
openxlsx
org.Hs.eg.db
packrat
parsnip
pbdZMQ
permute
phangorn
pheatmap
phytools
pillar
pixmap
pkgbuild
pkgconfig
pkgKitten
pkgload
plogr
plotmo
plotrix
pls
plyr
png
polyclip
polynom
PopGenome
praise
preprocessCore
prettycode
prettyunits
pROC
processx
prodlim
progress
promises
ProtGenerics
ps
purrr
quadprog
questionr
qvalue
R6
rappdirs
raster
RBGL
rcmdcheck
RColorBrewer
Rcpp
RcppArmadillo
RcppEigen
RcppParallel
RcppProgress
RcppRoll
RCurl
readr
readxl
recipes
rematch
remotes
repr
reprex
reshape
reshape2
rex
Rgraphviz
rjags
rlang
rlist
rmarkdown
Rmpi
RMySQL
robustbase
ROCR
roxygen2
RPostgreSQL
rprojroot
rsample
Rsamtools
rsconnect
RSQLite
rstan
rstanarm
rstantools
rstudioapi
rtracklayer
RUnit
rvcheck
rversions
rvest
S4Vectors
scales
scatterplot3d
segmented
selectr
sendmailR
seqinr
sessioninfo
sf
sfsmisc
shiny
shinyjs
shinystan
shinythemes
ShortRead
sm
snow
SnowballC
SNPRelate
som
sourcetools
sp
SparseM
spData
spdep
SQUAREM
StanHeaders
stopwords
stringi
stringr
SummarizedExperiment
survival
sva
sys
TeachingDemos
testit
testthat
threejs
tibble
tidygraph
tidymodels
tidyposterior
tidypredict
tidyr
tidyselect
tidytext
tidyverse
tikzDevice
timeDate
tinytex
tokenizers
topGO
triebeard
tune
tweenr
units
UpSetR
urltools
usethis
utf8
uuid
vctrs
vegan
VennDiagram
vioplot
viridis
viridisLite
visNetwork
webutils
whisker
withr
workflows
wTO
xfun
XML
xml2
xopen
xtable
xts
XVector
yaml
yardstick
zip
zlibbioc
zoo

Debian Packages installed especially for EVOP

(available on server and on the client PCs )
  • augustus
  • bcftools
  • beast2-mcmc
  • beast2-mcmc-doc
  • beast2-mcmc-examples
  • bowtie
  • bowtie2
  • bowtie2-examples
  • bowtie-examples
  • build-essential
  • bwa
  • cowsay
  • cufflinks
  • cutadapt
  • emboss-data
  • emboss-doc
  • emboss-explorer
  • emboss-test
  • exonerate
  • fastqc
  • fastx-toolkit
  • freebayes
  • gnuplot
  • gnuplot-doc
  • hisat2
  • hmmer
  • iqtree
  • jemboss
  • jupyter-notebook
  • mafft
  • mcl
  • mcl-doc
  • metaphlan2
  • metaphlan2-data
  • mrbayes
  • mrbayes-doc
  • mrbayes-mpi
  • mummer
  • mummer-doc
  • ncbi-blast+
  • picard-tools
  • plink1.9
  • proj-bin
  • proj-data
  • proteinortho
  • python3-biopython
  • python3-cutadapt
  • python3-gffutils
  • python3-pymummer
  • python3-pyvcf
  • python-biopython
  • python-biopython-doc
  • python-cutadapt
  • python-dev
  • python-gnuplot
  • python-pyvcf
  • python-pyvcf-examples
  • pyvcf
  • qgis
  • qgis-api-doc
  • qgis-common
  • qgis-mapserver
  • qgis-server
  • raxml
  • ray
  • ray-doc
  • ray-extra
  • repeatmasker-recon
  • rna-star
  • rstudio
  • segemehl
  • snakemake
  • sra-toolkit
  • stacks
  • stacks-web
  • subread
  • subread-data
  • trimmomatic
  • vcftools
  • vsearch
  • yaggo

There are, of course, more (general) Debian packages installed on the EVOP server and desktop PCs! To see the complete list, call dpkg -l" in the command line on one of the evop computers.
smile
Topic revision: r9 - 04 Mar 2020, IngmarCamphausen
 
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