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You are here: Foswiki>IT Web>ItServices>ItServicesProjects>ItServicesProjectsEvop (04 Mar 2020, IngmarUserTopic)Edit Attach
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 calledevop-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
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 nodeandorra.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-wideeduroam 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
- Manual for using
eduroamwith FU account (in German) - Manual for using
eduroamby guests of Freie Universität Berlin (in German) - …. (English versions?)
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) - WLAN Key gültig / valid 24.02.-08.03.2020:
...
(bitte beim Veranstalter erfragen! / please ask the workshop chairs! ) - WLAN Key gültig / valid 09.03.-22.03.2020:
...
(bitte beim Veranstalter erfragen! / please ask the workshop chairs! ))
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 )
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
dpkg -l" in the command line on one of the evop computers.
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