IT-Services::Evop

Info and manual page regarding the IT setup (hard- and software) for the EVOP 2026 workshop

Veranstalter, Organisation

mailto: Evop Veranstalter

• Prof. Dr. Katja Nowick, Professorin für Humanbiologie Freie Universität Berlin Institut für Zoologie
• Co-Organizer: Dr. Vladimir Jovanović Freie Universität Berlin, Bioinformatics Solution Center (BSC), Institut für Informatik, Humanbiologie, Institut für Biologie

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 for /srv/evop
• Backup - nightly mirroring of the content of the /srv/evop/software directory to a dedicated backup server without the NO_BACKUP folder.

IT-Services::Evop - Desktop PCs

• There are 28 desktop PCs available in the workshop venue:
  • OS: Linux (Debian "trixie")
  • CPU: Intel i5 (14. Generation)
  • 32 GB RAM
  • Graphics: RTX 4060
  • local storage: 500 GB NVMe SSD (in each PC)
  • 27" TFT-Monitor for each PC
• The desktop PCs are named

agnesi.imp.fu-berlin.de
breteuil.imp.fu-berlin.de
cauchy.imp.fu-berlin.de
euklid.imp.fu-berlin.de
euler.imp.fu-berlin.de
fenchel.imp.fu-berlin.de
germain.imp.fu-berlin.de
hamel.imp.fu-berlin.de
hayes.imp.fu-berlin.de
hypathia.imp.fu-berlin.de
jordan.imp.fu-berlin.de
kendall.imp.fu-berlin.de
kutta.imp.fu-berlin.de
lalla.imp.fu-berlin.de
landau.imp.fu-berlin.de
ludolph.imp.fu-berlin.de
neumann.imp.fu-berlin.de
peter.imp.fu-berlin.de
rellich.imp.fu-berlin.de
rudin.imp.fu-berlin.de
runge.imp.fu-berlin.de
stott.imp.fu-berlin.de
bigollo.imp.fu-berlin.de
napier.imp.fu-berlin.de
ptolemy.imp.fu-berlin.de
bala.imp.fu-berlin.de
harlech.imp.fu-berlin.de
tywyn.imp.fu-berlin.de

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

There is no backup done for the 28 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 VPN system with the course account you got.

IT-Services::Evop - WiFi access

For mobile computers/devices brought by the participants, you can connect them to the Internet via WiFi network (wireless LAN, WLAN) via eduroam: For people coming from instituions that participate in the world-wide eduroam, you can use your institutions account. Everybody else can use the course account for the workshop to use the eduroam WiFi network.

WiFi access via eduroam network

• Manual for using eduroam - overview (in German)
• Manual for using eduroam - details (in German)
• …. (English versions?)

Alternative: WiFi access via Free WiFi Berlin network

Connect to the WiFi network with the name (SSID) _Free_Wifi_Berlin. After connection you have to open a browser to accept the therms and conditions and then you can access the internet (but no course resources).

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/k00345678/ for user account k00345678 ). Additionally, we have created a "group folder" /srv/evop/ where you can deposit materials (documents, computation data) for the students. The directory is an exported NFS storage that is accessible from all desktop PCs, so example data etc. that is stored there is easily available on the 28 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: mailto: evop-support .

IT-Services::Evop - Software

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

Software packages manually installed

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

Name	Version	Homepage/Download
Admixture	1.3.0	https://github.com/NovembreLab/admixture
ASTRAL	5.7.1	java -jar /srv/evop/software/astral/Astral/astral.5.7.8.jar # 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
conda	24.5.0	/opt/conda/bin/conda init # from https://repo.anaconda.com/pkgs/misc/debrepo/conda stable main
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
uv	0.10.2	curl -LsSf https://astral.sh/uv/install.sh $pipe sh # user install to home # https://docs.astral.sh/uv/
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

admixr         BiocParallel     edgeR          ggiraph     graph           pdftools    SNPRelate             V8
AnnotationDbi  BiocVersion      enrichplot     ggnewscale  gson            pinfsc50    SparseArray           vcfR
aplot          biomaRt          fgsea          ggplotify   IRanges         qpdf        SummarizedExperiment  XVector
Biobase        Biostrings       filelock       ggtangle    KEGGREST        qvalue      tidydr                yulab.utils
BiocBaseUtils  clusterProfiler  gdsfmt         ggtree      limma           README.md   tidytree
BiocFileCache  DelayedArray     GenomeInfoDb   git2r       MatrixGenerics  S4Arrays    topGO
BiocGenerics   DESeq2           GenomicRanges  GO.db       memuse          S4Vectors   treeio
BiocManager    DOSE             ggfun          GOSemSim    org.Hs.eg.db    scatterpie  UCSC.utils

Debian Packages installed especially for EVOP

- freebayes - apptainer - augustus - bcftools - beast2-mcmc - beast2-mcmc-examples - bedtools - bowtie - bowtie2 - bowtie2-examples - bwa - cowsay - cufflinks - cutadapt - emboss-data - emboss-doc - emboss-explorer - emboss-lib - emboss-test - exonerate - fastqc - figtree - freebayes - gffread - gnuplot - gnuplot-doc - hisat2 - hmmer - iqtree - jemboss - libdbd-sqlite3-perl - libdbd-pg-perl - libemboss-acd-perl - libforks-perl - libgdal-dev - libgeos-dev - libgit2-dev - libinline-c-perl - libio-all-perl - libipc-signal-perl - libjellyfish-perl - libmagick++-dev - libpoppler-glib-dev - libpoppler-cpp-dev - libproj-dev - libsparsehash-dev - libssh2-1-dev - libtext-soundex-perl - libtool - libudunits2-dev - libxcomposite1 - libxcursor1 - libxi6 - libxrandr2 - libxss1 - libxtst6 - mafft - mcl - mcl-doc - metaphlan - metaphlan2-data - mrbayes - mrbayes-doc - mrbayes-mpi - multiqc - mummer - mummer-doc - picard-tools - proteinortho - python3-cutadapt - python3-gffutils - python3-gnuplot - python3-pandas - python3-pymummer - pyvcf - qgis - qgis-api-doc - qgis-common - qgis-server - r-cran-adegenet - r-cran-ape - r-cran-biocmanager - r-cran-ggplot2 - r-cran-magrittr - r-cran-mass - r-cran-phangorn - r-cran-pheatmap - r-cran-tidyverse - raxml - ray - ray-doc - ray-extra - repeatmasker-recon - rna-star - rstudio - samtools - seaview - segemehl - snakemake - stacks - subread - subread-data - trimmomatic - vcftools - vsearch

• yaggo

There are, of course, more (general) Debian packages installed on the desktop PCs! To see the complete list, call dpkg -l" in the command line on one of the evop computers.