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Nächste planmäßige Wartung:

Mittwoch, 4. März 2020


IT-Services::Evop

Informations- und Anleitungswebseite für die IT-Ausstattung (Hardware + Software) des EVOP 2020-Workshops
Info and manual page re: the IT setup (hard- and software) for the EVOP 2020 workshop

wip WORK IN PROGRESS


IT-Services::Evop - Login Server

Der zur Verfügung gestellte Server ist erreichbar unter dem Namen evop-login (DNS-Name 'evop-login.imp.fu-berlin.de') und läuft unter Linux (Debian "Buster"). Sein lokaler Storage-Bereich für Daten hat eine Größe von xxxx TB.
The server provided for the workshop is called evop-login (FQDN: 'evop-login.imp.fu-berlin.de'). It runs Debian "Buster" Linux. It has xxxx TB local storage.

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

Folgende Sicherungssysteme sind aktiv:
The following measures are in place and active:
  • RAID - Schutz vor physikalischem Festplattenausfall / protection in case of physical failure of single disks
  • Backup - nächtliches Kopieren des Inhaltes der Verzeichnisse unterhalb von /srv/ auf einen dezidierten Backup-Server / nightly mirroring of the content of the /srv/ directory to a dedicated backup server

IT-Services::Evop - Desktop PCs

  • Neben dem Login-Server stehen im Workshop-Raum 30 Desktop-PCs jeweils mit folgender Ausstattung zur Verfügung:
    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
  • Die Desktop-PCs heißen / 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 - Sicherung / Backup

ALERT! Von den Desktop-PCs erfolgt keine Datensicherung. / There is no backup done for the 30 desktop PCs.

IT-Services::Evop - WLAN-Zugang / WiFi access

Es stehen für mitgebrachte Geräte zwei Möglichkeiten zur Verfügung, wie diese per WLAN Internetzugang bekommen können: Für Workshop-Teilnehmende, deren Heimateinrichtung am eduroam -Verbund teilnimmt oder die für die Veranstaltung mit einem FU-Account ausgestattet wurden, kann das eduroam -Funknetz benutzt werden. Darüberhinaus steht den Workshop-Teilnehmern ein temporäres WLAN conference für die Zeit des Workshops zur Verfügung.

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: WLAN-Zugang via eduroam / WiFi access via eduroam network

Alternative 2: WLAN-Zugang via conference -Netz / WiFi access via conference network

Einbuchen in das WLAN-Netz mit dem Namen (SSID) conference . Es muss dann ein Zugangs-Schlüssel eingegeben werden, der für 14 Tage gültig ist (und daher im Verlauf des Workshops einmal gewechselt werden muss!).
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 xxxx.-xxxx.03.2020: ...
    (bitte beim Veranstalter erfragen! / please ask the workshop chairs! )
  2. WLAN Key gültig / valid xxx-xxxx.03.2020: ...
    (bitte beim Veranstalter erfragen! / please ask the workshop chairs! ))

Weitere Hinweise zur Benutzung des conference -WLANs finden Sie hier / further details on using the conference WiFi can be found here:

IT-Services::Evop - Software

Der Login-Server und die Desktop-PCs laufen unter Debian Linux, Release "Buster". Auf ihnen steht folgende Biocomputing-spezifische Software-Ausstattung zur Verfügung:
The login server and the desktop PCs are running Debian Linux "Buster" and provide the following biocomputing specific software environment:

Software-Pakete / software packages

SoftwareSorted descending Version Source
vsearch 2.12.0 https://github.com/torognes/vsearch
VEP   https://www.ensembl.org/info/docs/tools/vep/index.html
vcftools   https://vcftools.github.io/man_latest.html
vcflib   https://github.com/vcflib/vcflib
trimmomatic   http://www.usadellab.org/cms/?page=trimmomatic
TreeMix   https://bitbucket.org/nygcresearch/treemix/wiki/Home
transeq   http://emboss.sourceforge.net/apps/cvs/emboss/apps/transeq.html
subread package   http://subread.sourceforge.net/
Structure v2.3.4 https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v2.3.4/html/structure.html
STAR   https://github.com/alexdobin/STAR
Stacks 2 2.3e http://catchenlab.life.illinois.edu/stacks/
Stacks v1.48 http://catchenlab.life.illinois.edu/stacks/
http://catchenlab.life.illinois.edu/stacks/source/stacks-1.48.tar.gz
SRA toolkit   https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
seqret   https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/
segemehl   http://www.bioinf.uni-leipzig.de/Software/segemehl/
samtools 1.7 http://www.htslib.org/, Sourcen: https://github.com/samtools/samtools/releases/download/1.7/samtools-1.7.tar.bz2
Rstudio   https://www.rstudio.com/products/rstudio/download/
rnacount   https://github.com/qbicsoftware/rnacount
Repeat Masker   http://www.repeatmasker.org/RMDownload.html
ray meta   https://github.com/sebhtml/ray
RAxML   https://github.com/stamatak/standard-RAxML
R    
qiime2   https://qiime2.org/
Qgis   https://qgis.org/en/site/forusers/download.html
pyVCF   https://github.com/jamescasbon/PyVCF
pyspark-notebook   https://hub.docker.com/r/jupyter/pyspark-notebook/
PREQUAL   https://github.com/simonwhelan/prequal
plink 1.9 https://www.cog-genomics.org/plink/1.9/
PICARD 2.8.2 https://broadinstitute.github.io/picard/
PHYLOBAYES MPI   https://github.com/bayesiancook/pbmpi
(http://megasun.bch.umontreal.ca/People/lartillot/www/downloadmpi.html)
PGDSpider   http://www.cmpg.unibe.ch/software/PGDSpider/
pear 0.9.11 https://www.h-its.org/downloads/pear-academic/
http://www.exelixis-lab.org/web/software/pear
Orthofinder   http://www.stevekellylab.com/software/orthofinder
mummer4   https://github.com/mummer4/mummer
MultiQC 1.8.dev0 https://multiqc.info/
MRBAYES   http://nbisweden.github.io/MrBayes/download.html
metaphlan2   http://huttenhower.sph.harvard.edu/metaphlan2
megahit   https://github.com/voutcn/megahit
maker   http://yandell.topaz.genetics.utah.edu/maker_downloads/F625/EB04/C67D/326EDA5692CF4F71A69A161EBB81/maker-2.31.9.tgz
Mafft   https://mafft.cbrc.jp/alignment/software/linux.html
Jupyter notebook   https://hub.docker.com/r/jupyter/
jmodeltest2   https://github.com/ddarriba/jmodeltest2
IQTREE   http://www.iqtree.org/#download
igvtools + IGV Genome browser   https://software.broadinstitute.org/software/igv/
get_homologues   https://github.com/eead-csic-compbio/get_homologues
genscan   http://genes.mit.edu/GENSCAN.html
Genepop   https://kimura.univ-montp2.fr/~rousset/Genepop.htm
GATK 3.6 https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.6-0-g89b7209
freebayes   https://github.com/ekg/freebayes
fastx-Toolkit   http://hannonlab.cshl.edu/fastx_toolkit/
fastStructure   https://github.com/rajanil/fastStructure
fastsimcoal26   http://cmpg.unibe.ch/software/fastsimcoal2/
fastQC   http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
fastq-pair   https://github.com/linsalrob/fastq-pair
FastME 2.1.5 https://gite.lirmm.fr/atgc/FastME/
exonerate   https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
duk   http://duk.sourceforge.net/
Docker CE   via SALT: classes:docker.ce
Distruct   https://rosenberglab.stanford.edu/distruct.html
cutadapt   https://cutadapt.readthedocs.io/en/stable/
Cufflinks   https://github.com/cole-trapnell-lab/cufflinks
cowsay   cowsay
Canu (Assembler) v1.8 https://github.com/marbl/canu
Canu (Assembler)   https://github.com/marbl/canu
bwa   http://bio-bwa.sourceforge.net/
bowtie2   http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
bowtie   http://bowtie-bio.sourceforge.net/bowtie2/
bokeh   https://bokeh.pydata.org/en/0.10.0/docs/user_guide/notebook.html
BMGE   ftp://ftp.pasteur.fr/pub/gensoft/projects/BMGE/
BLAST+   https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
blast   https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
BioPython installed with conda   installiertes anaconda
beast2 2.4.8 http://www.beast2.org/
bcftools 1.6 https://github.com/samtools/bcftools/releases/download/1.6/bcftools-1.6.tar.bz2
Bayescan 2.1 http://cmpg.unibe.ch/software/BayeScan/download.html
bamaddrg   https://github.com/ekg/bamaddrg
B dadi   https://bitbucket.org/gutenkunstlab/dadi
augustus   http://bioinf.uni-greifswald.de/augustus/
ASTRAL   https://github.com/smirarab/ASTRAL
arlsumstats   http://cmpg.unibe.ch/software/arlequin35/Arl35Downloads.html
arlecore   http://cmpg.unibe.ch/software/arlequin35/Arl35Downloads.html
anaconda Python 3   Teil der anaconda-Installation
anaconda   https://www.anaconda.com/download/#linux
abctoolbox   http://cmpg.unibe.ch/software/ABCtoolbox/

R packages

  • acepack
  • ade4
  • adegenet
  • agricolae
  • ape
  • assertthat
  • base64enc
  • Biostrings
  • bitops
  • boot
  • catools
  • chron
  • class
  • cluster
  • coda
  • codetools
  • CoDiNA
  • colorspace
  • crayon
  • data.table
  • dbi
  • deldir
  • dichromat
  • digest
  • doparallel
  • dplyr
  • evaluate
  • foreach
  • foreign
  • formula
  • futile.logger
  • futile.options
  • gdata
  • genepop
  • getopt
  • ggplot2
  • gmodels
  • gplots
  • gridbase
  • gridextra
  • gtable
  • gtools
  • highr
  • hmisc
  • htmltable
  • htmltools
  • httpuv
  • httr
  • igraph
  • irlba
  • iterators
  • jsonlite
  • kernsmooth
  • knitr
  • labeling
  • lambda.r
  • lattice
  • latticeextra
  • lazyeval
  • learnbayes
  • littler
  • magrittr
  • markdown
  • MASS
  • matrix
  • memoise
  • mgcv
  • mime
  • munsell
  • nlme
  • nmf
  • nnet
  • ouch
  • permute
  • phytools
  • pkgkitten
  • pkgmaker
  • plyr
  • PopGenome
  • r6
  • rcolorbrewer
  • rcpp
  • rcurl
  • registry
  • reshape2
  • rlist
  • rngtools
  • rpart
  • rsqlite
  • rstudioapi
  • scales
  • segmented
  • seqinr
  • shiny
  • sm
  • snow
  • sourcetools
  • sp
  • spatial
  • spdep
  • stringi
  • stringr
  • survival
  • tibble
  • tidyverse
  • vegan
  • vioplot
  • viridis
  • wTO
  • xml
  • xml2
  • xtable
  • yaml

(all from https://cran.r-project.org/web/packages/)

Bioconductor packages

  • annotate
  • annotationdbi
  • biobase
  • biocgenerics
  • biocparallel
  • biomart
  • biomaRt
  • biostrings
  • DESeq2
  • EdgeR
  • genefilter
  • geneplotter
  • genomeinfodb
  • genomicranges
  • iranges
  • limma
  • org.Hs.eg.db
  • preprocessCore
  • s4vectors
  • summarizedexperiment
  • topGO
  • xvector

(all from https://bioconductor.org/packages/)

Debian Packages

... (TBA)
Topic revision: r2 - 31 Jan 2020, IngmarCamphausen
 
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