ceuadmin

The CEU software repository is here, /usr/local/Cluster-Apps/ceuadmin/ (CEUADMIN).

ceuadmin

Some source packages are kept at /rds/project/rds-4o5vpvAowP0/software (~/rds/software if defined).

Entries

The current list is as follows,

  [1] "ABCtoolbox"             "akt"                    "allegro"                "alpine"
  [5] "alsa-lib"               "Anaconda2"              "Anaconda3"              "angsd"
  [9] "annovar"                "AnythingLLMDesktop"     "apidog"                 "aria2"
 [13] "augeas"                 "autoconf"               "automake"               "awscli"
 [17] "axel"                   "bash-language-server"   "bazel"                  "bcftools"
 [21] "Beagle"                 "bedops"                 "bedtools2"              "bgen"
 [25] "binutils"               "biobank"                "BitNet"                 "blat"
 [29] "blupf90"                "boltlmm"                "boost"                  "brotli"
 [33] "busybox"                "BWA"                    "C2S-Scale"              "caddy"
 [37] "CaVEMaN"                "CAVIAR"                 "CAVIARBF"               "cbindgen"
 [41] "ccal"                   "ccphylo"                "chrome"                 "chromium"
 [45] "circos"                 "citeproc"               "clang"                  "claude-code"
 [49] "cli"                    "clues2"                 "cmake"                  "cmocka"
 [53] "codex-cli"              "comet"                  "copilot-cli"            "cppunit"
 [57] "crossmap"               "crux"                   "cryptopp"               "cryptsetup"
 [61] "curl"                   "Cytoscape"              "delphi"                 "deno"
 [65] "DEPICT"                 "device-mapper"          "diann"                  "DjVuLibre"
 [69] "docbook2X"              "docker"                 "DosageConverter"        "dotnet"
 [73] "DrugAssist"             "dump_syms"              "Eagle"                  "edge"
 [77] "edit"                   "edlib"                  "enchant"                "ensembl-vep"
 [81] "exiv2"                  "exomeplus"              "expat"                  "FastQTL"
 [85] "fcGENE"                 "ffmpeg"                 "fgwas"                  "findlib"
 [89] "finemap"                "firefox"                "FlashLFQ"               "flashpca"
 [93] "fly"                    "fNUMT"                  "fossil"                 "fpc"
 [97] "FragPipe"               "fraposa_pgsc"           "freesurfer"             "fresh"
[101] "fribidi"                "fsc2"                   "GARFIELD"               "gatk"
[105] "gcc"                    "gcc-toolset"            "gcloud"                 "gcta"
[109] "gdal"                   "gdc"                    "geany"                  "GEM"
[113] "gemini-cli"             "GEMMA"                  "GENIE"                  "Genotype-Harmonizer"
[117] "geos"                   "gettext"                "gh"                     "ghc"
[121] "ghostscript"            "git"                    "git-extras"             "GitKraken"
[125] "git-lfs"                "glib"                   "glibc"                  "globusconnectpersonal"
[129] "glpk"                   "gmp"                    "gnutls"                 "go"
[133] "googletest"             "graphene"               "GraphicsMagick"         "GreenAlgorithms4HPC"
[137] "gsl"                    "gsutil"                 "gtk+"                   "gtksourceview"
[141] "gtool"                  "haplogrep"              "hap.py"                 "hapstat"
[145] "helix"                  "hermes-agent"           "hivex"                  "hpg"
[149] "htslib"                 "hunspell"               "icu"                    "ImageJ"
[153] "ImageMagick"            "impute"                 "impute5"                "inetutils"
[157] "inkscape"               "InstaNovo"              "IonQuant"               "JabRef"
[161] "JAGS"                   "jasper"                 "jbig2enc"               "jq"
[165] "json-c"                 "KentUtils"              "KING"                   "kojak"
[169] "krb5"                   "lapack"                 "ldc2"                   "ldsc"
[173] "LDstore"                "LEMMA"                  "leptonica"              "lib64"
[177] "libarchive"             "libarrow"               "libcares"               "libgcrypt"
[181] "libgeotiff"             "libgit2"                "libglvnd"               "libiconv"
[185] "libidn2"                "libjpeg-turbo"          "libntlm"                "libpng"
[189] "libseccomp"             "libsodium"              "libssh"                 "libssh2"
[193] "libuv"                  "libvips"                "libxml2"                "libxslt"
[197] "linux"                  "llama.cpp"              "llm"                    "locuszoom"
[201] "LVM2"                   "MAGENTA"                "magma"                  "Mango"
[205] "marksman"               "MaxQuant"               "Mega2"                  "metal"
[209] "MetaMorpheus"           "micromamba"             "Miniconda3"             "miniforge3"
[213] "mitoscape"              "mity"                   "MONSTER"                "MORGAN"
[217] "MR-MEGA"                "msamanda"               "MsCAVIAR"               "MSFragger"
[221] "MS-GF+"                 "msms"                   "MToolBox"               "MUMmer"
[225] "nano"                   "nasm"                   "ncbi-vdb"               "ncurses"
[229] "netbeans"               "nettle"                 "nextflow"               "nginx"
[233] "NLopt"                  "node"                   "nspr"                   "ntlm"
[237] "NUMTFinder"             "ocaml"                  "ollama"                 "oniguruma"
[241] "opam"                   "OpenClaw"               "openjdk"                "OpenMS"
[245] "openssh"                "openssl"                "osca"                   "p7zip-zstd"
[249] "PAINTOR"                "pandoc"                 "pandoc-citeproc"        "pango"
[253] "parallel"               "Pascal"                 "patchelf"               "pcre2"
[257] "pdf2djvu"               "pdfjam"                 "peer"                   "Perseus"
[261] "pgsc_calc"              "PGS-CSx"                "phenoscanner"           "PhySO"
[265] "Pi"                     "picard"                 "pigz"                   "pkg-config"
[269] "plink"                  "plink-bgi"              "plinkseq"               "pngquant"
[273] "podman"                 "PoGo"                   "polyphen"               "poppler"
[277] "popt"                   "postman"                "proj"                   "PRSice"
[281] "pspp"                   "pulsar"                 "PWCoCo"                 "pwiz"
[285] "python"                 "qctool"                 "qemu"                   "qpdf"
[289] "qt"                     "qtcreator"              "QTLtools"               "quarto"
[293] "quicktest"              "R"                      "raremetal"              "rclone"
[297] "readline"               "regenie"                "regtools"               "relate"
[301] "RHHsoftware"            "RSEM"                   "rst2pdf"                "rstudio"
[305] "rtg-tools"              "rtmpdump"               "ruby"                   "rust"
[309] "sage"                   "samtools"               "Scala"                  "scGPT"
[313] "scl-utils"              "selscan"                "seqkit"                 "SEQPower"
[317] "shapeit"                "shapeit5"               "shellcheck"             "simNGS"
[321] "singularity"            "SMR"                    "snakemake"              "sniffles"
[325] "SNP2HLA"                "snptest"                "spread-sheet-widget"    "spyder"
[329] "sqlite"                 "sra-tools"              "sshpass"                "ssw"
[333] "STAR"                   "stata"                  "SurvivalAnalysis"       "SurvivalKit"
[337] "SuSiEx"                 "SVanalyzer"             "Swift"                  "SYMPHONY"
[341] "Synapse"                "tabix"                  "tandem"                 "tatami"
[345] "tesseract"              "texinfo"                "ThermoRawFileParser"    "ThermoRawFileParserGUI"
[349] "thunderbird"            "tidy"                   "tiff"                   "trinculo"
[353] "trousers"               "truvari"                "Typora"                 "unbound"
[357] "uv"                     "vala"                   "VarScan"                "vce"
[361] "vcftools"               "vdo"                    "VEGAS2"                 "verifyBamID"
[365] "VirtualBox"             "VSCode"                 "VSCodium"               "vte"
[369] "wasi-sdk"               "Windsurf"               "wine"                   "wombat"
[373] "wrk"                    "xpdf"                   "yaml-cpp"               "Zettlr"
[377] "Zotero"                 "zstd"

These are wrapped up as :star::star::star: modules :star::star::star:.

The original list prior to mid-November 2022 is given below1.

Usage

We illustrate with pspp. A brief description of a module is available with

module help ceuadmin/pspp

and the module is loaded and graphical user interface (GUI)2 started with

module load ceuadmin/pspp
psppire

for version 2.0.1. Once the job is done, one can restore the previous environment with

module unload ceuadmin/pspp

Note that module add/rm is equivalent to module load/unload.

Some modules are based on compiled Java (.jar) which can be called directly but it is handy to use preset environment variables, e.g.,

module load ceuadmin/picard
java -jar ${PICARD_HOME}/picard.jar --help

A full list of module subcommands is available with module help as detailed here for 3.2.9 – cclake uses version 3.2.10 (2012-12-21) while icelake uses 4.5.2 (2020-07-30). In particular, module whatis ceuadmin/ensembl-vep indicates usage regarding build37/build38 setup for the loftee plugin used in loss of function (LoF) annotation.

CEU users

CEU users will be able to use ANNOVAR, ensembl-vep, OpenMS (ceuadmin/OpenMS/3.4.0 now available for CSD3 users), phenoscanner (MySQL server yet to resolve), polyphen, KentUtils/MAGMA/Pascal/VEGASV2/fgwas/locuszoom linking internal projects/personal space (additional requests need to be made).

R

A large collection of R packages (1,838 as of 22/7/2026, esp. with availability of major machine learning packages) is linked with the latest R distribution, 4.6.1; there are also packages (CRAN: DescTools, Rfast, Rfast2, SKAT, rcompanion, rms – which requires stringi herein, riskRegression – which requires rms; Bioconductor: BiocSingular, DropletUtils, DSS, beachmat, bsseq, scater, scuttle, xcms, xgboost) under 4.6.1-gcc11. Earlier versions such as sf, caTools, lme4, lwgeom, terra, riskRegression, rms, scater, scuttle, SKAT, TMB were removed when they appear for 4.6.1-gcc11. For Rserve 1.8-15, openssl/3.3.0-dev appears working. The package paws.analytics 0.10.0 is furnished with SLURM3. The failed package is arrow 25.0.0.

It is possible to use packages built under gcc11, e.g., rms as in

module load ceuadmin/R
module load gcc/11.3.0/gcc/4zpip55j
R CMD build --compact-vignettes=both --md5 --resave-data --log gaawr2

Lately, 4.6.1-gcc12 is also created based on ceuadmin/gcc/12.5.0 and ceuadmin/gcc-toolset/12. The highest version of GLIBCXX is found from

strings /usr/local/software/spack/spack-views/rocky8-icelake-20220710/gcc-11.3.0/gcc-11.3.0/4zpip55j2rww33vhy62jl4eliwynqfru/lib64/libstdc++.so.6 \
grep '^GLIBCXX_' \
sort -V \
tail -1
strings /usr/local/Cluster-Apps/ceuadmin/gcc/12.5.0/lib64/libstdc++.so.6 | grep ^GLIBCXX_ | sort -V | tail -1

giving GLIBCXX_3.4.29 and GLIBCXX_3.4.30, respectively.

Additionally,

  • xcms also requires ncdf4 and associate module, e.g., module load netcdf-c/4.8.1/gcc/intel-oneapi-mpi/2765z52t.
  • with recent work on gdal/3.0.4, sf 1.0-21 has been compiled enabling raster 3.6-32, stars 0.6-8, terra 1.8-50 (not 1.8-54 but it appears working with module gdal/3.7.0-icl), maptiles 0.10.0 / tmap 4.1. Moreover, rgdal has been replaced with sf and withdrawn from CRAN according to information there.
  • arrow/22.0.0.1 is available for gcc/8.5 but not arrow/23.0.0 (C++20 compiler OK with gcc/12.1.0 but GLIBC2.28 under CentOS 8 is too old); see https://arrow.apache.org/docs/r/articles/install.html.

It is easy to point to them, e.g.,

export HPC_WORK=/rds/user/$USER/hpc-work/
export RDS=/rds/project/jmmh2/rds-jmmh2-public_databases/software
export R_LIBS=${RDS}/R:${RDS}/R-gcc11

or possible to have your own installations based on these, e.g., through creation of a modified Makefile with altered prefix followed by make install -f <modified Makefile>.

The following script tests for loading of dplyr:

export RDS=/rds/project/jmmh2/rds-jmmh2-public_databases/software
export PATH=${PATH}
export R_LIBS=${RDS}:${RDS}/R
Rscript -e 'suppressMessages(library(dplyr));cat("OK!\n")'

It appears clumsy to do these every time, so an attempt is made to have them in a module, namely

module load ceuadmin/R/latest
which R
echo $R_LIBS
Rscript -e 'suppressMessages(library(dplyr));cat("OK!\n")'

Inside R, one can check paths with .libPaths(). It is also handy to re-install the small number of packages in R-gcc11 with install.packages(dir()) at its folder but BiocManager::install(c("beachmat", "BiocSingular", "DropletUtils", "scater", "scuttle")).

A final note regarding UBSAN-Clang like setup for R CMD check --as-cran, in the case of gap_1.15.tar.gz it is noted here: https://github.com/jinghuazhao/R/tree/master/docs.

Python

There are many sources,

  1. miniconda37/. Collections for Miniconda3 which is appropriate for a variety of software including its distribution of R.
  2. py2.7/. Collections for Python 2.7.
  3. py38/. Collections for Python 3.8.
  4. py3.11/. Collections for Python 3.11.

One can use source command to load/install packages, e.g., source ${RDS}/py38/bin/activate. A list of modules can be checked with

conda list
pip list

for Minicoda and Python, respectively.

Note that finally VIRTUAL_ENV is used to replace PYTHONPATH in earlier modules.

Non-CEU users

Most software are available for all CSD3 users, only limited by software with excessive size / reference data – which ideally will be available from /rds/project/jmmh2/software but now /rds/project/jmmh2/rds-jmmh2-public_databases/software as a trade-off. These can largely be seen as sources which are used to build the reoository given above.

Please drop an email to jhz22@medschl.cam.ac.uk for access.

Module creation

The following example shows how to set up a module,

#!/bin/bash

mkdir tmp-xz
cd tmp-xz
wget http://tukaani.org/xz/xz-5.2.2.tar.gz
tar zxvf xz-5.2.2.tar.gz
cd xz-5.2.2
mkdir -p /usr/local/Cluster-Apps/xz/5.2.2
export PREFIX=/usr/local/Cluster-Apps/xz/5.2.2
./configure --prefix=$PREFIX
make
make check
sg swinst 'make install'

cat << 'EOL' > /usr/local/Cluster-Config/modulefiles/xz/5.2.2
#%Module -*- tcl -*-
##
## modulefile
##
proc ModulesHelp { } {

  puts stderr "\tXZ Utils is free general-purpose data compression software with a high compression ratio.\n"
  puts stderr "\tInstalled under: /usr/local/Cluster-Apps/xz/5.2.2
     Hompage:http://tukaani.org/xz/"

}

module-whatis "xz free general-purpose data compression"

conflict xz
set               root                  /usr/local/Cluster-Apps/xz/5.2.2
prepend-path      PATH                  $root/bin
prepend-path      MANPATH               $root/man
prepend-path      LD_LIBRARY_PATH       $root/lib
prepend-path      LIBRARY_PATH          $root/lib
prepend-path      FPATH                 $root/include
prepend-path      CPATH                 $root/include
prepend-path      INCLUDE               $root/include
setenv            XZ_HOME               $root
EOL

The module is made visible through environment variable MODULEPATH. Note that there will be permission issue for a user, however, to make changes to /usr/local/Cluster-Apps.

The module files are defined at /usr/local/Cluster-Config/modulefiles/ceuadmin. Most software stay with gcc/6 due to many dependencies of built modules; when required it can be enabled with module load gcc/6; however packages could also require libgfortran.so.5 as in gcc/9 – as a compromise one can amend .bashrc to include lines such as export LD_LIBRARY_PATH=/usr/local/software/master/gcc/9/lib64:$LD_LIBRARY_PATH.

Footnotes

Further information is avaiiable from /usr/local/Cluster-Apps/ceuadmin/doc/ceuadmin.md, ceuadmin.html.

More detailed diagrams on recently added genetics/proteomics and generic software are as follows,

Genetics Generic

noting that the importance of software is purely random according to \(Poisson(N,\lambda)\) where \(N\) is the number of entries, \(\lambda=3\).

  1. The original list was a mixture of modules and directories as follows,

    bgenix/               impute_v2.3.2_x86_64_static/  plink/                        R/                 Raremetal_linux_executables/        snptest_new/
biobank/              interval/                     plink_1.90_beta/              raremetal_4.13/    Raremetal_linux_executables.tgz     source/
boltlmm/              JAGS/                         plink_bgi_Dev/                raremetal_4.13.3/  raremetal.log                       stata/
boltlmm_2.2/          LDstore/                      plink-bgi_linux_x86_64_may/   raremetal_4.13.4/  regenie/                            tabix/
crossmap/             locuszoom/                    plink_linux_x86_64_beta2a/    raremetal_4.13.5/  samtools-1.10.tar.bz2               temp/
exomeplus/            magma/                        plink_linux_x86_64_beta3.32/  raremetal_4.13.7/  samtools_1.2/                       vcftools/
gcta/                 MAGMA_Celltyping/             plinkseq-0.08-x86_64/         raremetal_4.13.8/  shapeit.v2.r790.RHELS_5.4.dynamic/  vcftools_ps629/
gtool_v0.7.5_x86_64/  metabolomics/                 plinkseq-0.10/                raremetal_4.14.0/  snptest/
hpg/                  metal/                        pspp/                         raremetal_4.14.1/  snptest_2.5.2/
htslib/               metal_updated/                qctool_v1.4-linux-x86_64/     raremetal_BPGen/   snptest_2.5.4_beta3/

    A grep of recent add-ons in the Genetics/Proteomics category is as follows,

    Date Add.ons Category
    2022-10-22 snptest/2.5.6 Genetics
    "" qctool/2.0.8 Genetics
    "" gcta/1.94.1 Genetics
    "" KING/2.1.6 Genetics
    "" LDstore/2.0 Genetics
    "" shapeit/3 Genetics
    "" vcftools/0.1.16 Genetics
    "" finemap/1.4 Genetics
    2022-10-23 quicktest/1.1 Genetics
    "" samtools/1.11 Genetics
    "" bcftools/1.12 Genetics
    "" MORGAN/3.4 Genetics
    "" METAL/2020-05-05r Genetics
    "" regenie/3.2.1 Genetics
    "" GEMMA/0.98.5 Genetics
    "" htslib/1.12 Genetics
    "" fcGENE/1.0.7 Genetics
    "" SMR/1.0.3 Genetics
    "" FastQTL/2.165 Genetics
    2022-10-26 circos/0.69-9 Genetics
    "" bgen/1.1.7 Genetics
    "" DosageConverter/1.0.0 Genetics
    "" QTLtools/1.3.1-25 Genetics
    "" blat/37x1 Genetics
    "" bedtools2/2.29.2 Genetics
    "" bedops/2.4.41 Genetics
    2022-11-03 Beagle/3.0.4 Genetics
    2022-11-08 CrossMap/0.6.4 Genetics
    "" SurvivalKit/6.12 Genetics
    "" PRSice/2.3.3 Genetics
    2022-11-09 qctool/2.2.0 Genetics
    2022-11-10 CaVEMaN/1.01-c1815a0 Genetics
    "" akt/0.3.3 Genetics
    "" MsCAVIAR/0.6.4 Genetics
    "" CAVIAR/2.2 Genetics
    "" MONSTER/1.3 Genetics
    "" osca/0.46 Genetics
    "" LEMMA/1.0.4 Genetics
    "" CAVIARBF/0.2.1 Genetics
    2022-11-11 PAINTOR/3.0 Genetics
    2022-11-14 MR-MEGA/0.2 Genetics
    2022-11-16 SNP2HLA/1.0.3 Genetics
    "" STAR/2.7.10b Genetics
    "" Mega2/6.0.0 Genetics
    2022-11-19 ensembl-vep/104 Genetics*
    "" OpenMS/3.0.0 Genetics*
    "" polyphen/2.2.2 Genetics*
    "" ANNOVAR/24Oct2019 Genetics*
    "" MAGENTA/vs2_July2011 Genetics*
    "" GARFIELD/v2 Genetics*
    "" KentUtils/2022-11-14 Genetics*
    2022-11-20 Genotype-Harmonizer/1.4.25 Genetics
    2022-11-21 locuszoom/1.4 Genetics*
    "" DEPICT/v1_rel194 Genetics*
    "" MAGMA/1.10 Genetics*
    "" Pascal/v_debut Genetics*
    "" VEGAS2/2.01.17 Genetics*
    "" fgwas/0.3.6 Genetics*
    2022-12-04 phenoscanner/v2 Genetics*
    2022-12-07 SurvivalAnalysis/2016-05-09 Genetics
    2023-01-03 Eagle/2.4.1 Genetics
    2023-01-05 GEM/1.4.5 Genetics
    2023-02-01 GENEHUNTER/2.1_r6 Genetics
    2023-03-14 regenie/3.2.5 Genetics
    2023-03-24 PoGo/1.0.0 Genetics
    2023-03-31 PWCoCo/2023-03-31 Genetics
    2023-04-02 regenie/3.2.5.3 Genetics
    2023-04-04 PWCoCo/1.0 Genetics
    2023-06-02 regenie/3.2.7 Genetics
    2023-06-06 allegro/2.0f Genetics
    2023-06-19 plink-ng/2.00a3.3 Genetics
    2023-06-26 RHHsoftware/0.1 Genetics
    2023-07-28 PWCoCo/1.1 Genetics
    2023-08-02 regenie/3.2.9 Genetics
    2023-08-06 finemap/1.4.2 Genetics
    2023-09-27 ncbi-vdb/3.0.8 Genetics
    "" sra-tools/3.0.8 Genetics
    "" gatk/4.4.0.0 Genetics
    2023-11-24 ldsc/1.0.1 Genetics
    2023-11-30 gdc/1.6.1-1.0.0 Genetics
    2023-12-20 verifyBamID/1.1.3 Genetics
    2023-12-21 verifyBamID/2.0.1 Genetics
    2023-12-27 regtools/1.0.0 Genetics
    "" VarScan/2.4.6 Genetics
    2024-01-08 picard/3.1.1 Genetics
    "" plink/2.0_20240105 Genetics
    2024-01-19 htslib/1.19 Genetics
    2024-01-24 fraposa_pgsc/0.1.0 Genetics
    "" pgsc_calc/2.0.0-alpha.4 Genetics
    2024-04-22 peer/1.3 Genetics
    2024-06-04 pwiz/3_0_24156_80747de Proteomics
    2024-06-09 crux/4.2 Proteomics
    "" DIA-NN/1.8.1 Proteomics
    2024-06-11 crux/4.1 Proteomics
    "" pwiz/3_0_24163_9bfa69a-wine Proteomics
    2024-06-11 seqkit/2.8.2 Proteomics
    "" FlashLFQ/1.2.6 Proteomics
    "" MetaMorpheus/1.0.5 Proteomics
    2024-06-25 msms/3.2rc-b163 Genetics
    2024-07-13 msamanda/3.0.21.532 Proteomics
    2024-07-31 tandem/2017.2.1.4 Proteomics
    2024-08-11 comet/2024.01.1 Proteomics
    "" kojak/2.1.0 Proteomics
    "" kojak/1.5.5 Proteomics
    "" kojak/2.0.0a22 Proteomics
    2024-08-12 MS-GF+/2024.03.26 Proteomics
    2024-08-14 ThermoRawFileParser/1.4.4 Proteomics
    "" ThermoRawFileParserGUI/1.7.4 Proteomics
    "" FragPipe/22.0 Proteomics
    2024-08-15 MSFragger/4.1 Proteomics
    "" IonQuant/1.10.27 Proteomics
    2024-08-20 htslib/1.20 Genetics
    "" bcftools/1.20 Genetics
    "" samtools/1.20 Genetics
    2024-08-23 qpdf/11.9.1 Generic
    2024-09-01 MaxQuant/2.6.4.0 Proteomics
    "" Perseus/2.1.2.0 Proteomics
    2024-10-13 sage/0.14.7 Proteomics
    2025-03-18 OpenMS/3.4.0 Proteomics
    2025-03-22 diann/2.0.2 Proteomics
    2025-04-04 InstaNovo/1.1.1 Proteomics
    2025-04-05 InstaNovo/1.1.1-GPU Proteomics
    2025-04-07 scGPT/0.2.4 Single cell
    "" scanpy/1.11.1 Single cell
    2025-04-16 diann/2.1.0 Proteomics
    2025-04-23 gcta/1.94.4 Genetics
    2025-05-03 GENIE/1.1.1 Genetics
    2025-05-06 SuSiEx/1.1.2 Genetics
    2025-05-09 PGS-CSx/1.1.0 Genetics
    2025-05-14 RSEM/1.3.3 Genetics
    2025-05-15 BWA/0.7.19 Genetics
    2025-07-14 edlib/1.2.7 Genetics
    "" MUMmer/4.0.1 Genetics
    2025-07-15 SVanalyzer/0.36 Genetics
    2025-07-16 sniffles/2.2 Genetics
    "" SEQPower/1.1.0 Genetics
    2025-07-18 truvari/5.3.0 Genetics
    2025-07-19 hap.py/0.3.15 Genetics
    "" rtg-tools/3.13 Genetics
    2025-08-05 qctool/2.2.5 Genetics
    "" MToolBox/1.2.1 Genetics
    2025-08-10 haplogrep/2.4.0 Genetics
    "" haplogrep/3.2.2 Genetics
    2025-08-11 flashpca/2.0 Genetics
    2025-08-13 fNUMT/1.1 Genetics
    "" NUMTFinder/0.5.5 Genetics
    "" simNGS/1.7 Genetics
    2025-08-18 impute5/1.2.0 Genetics
    "" shapeit5/5.1.1 Genetics
    2025-09-01 selscan/2.1 Genetics
    "" angsd/0.940 Genetics
    2025-09-03 hapstat/3.0 Genetics
    2025-09-04 relate/1.2.3 Genetics
    "" clues2/github Genetics
    2025-09-05 fsc2/2.8.0 Genetics
    2025-09-09 mitoscape/1.0 Genetics
    2025-09-11 mity/2.0.1 Genetics
    2025-10-23 ccphylo/0.8.5 Genetics
    2026-04-01 gcta/1.95.1 Genetics
    2026-06-08 wombat/26-05-2025 Genetics
    "" vce/6 Genetics
    "" blupf90/2.75 Genetics

    * CEU or approved users only – when not indicated can be found out from the folder associated with a module. ↩

  2. GUI

    As GUI-based programs claim more computing resources, it is recommended that they are only used occasionally, e.g., calling back GitHub sessions. ↩

  3. paws.analytics

    #!/usr/bin/env bash

#SBATCH --job-name=_cran
#SBATCH --account PETERS-SL3-CPU
#SBATCH --partition icelake-himem
#SBATCH --mem=28800
#SBATCH --time=12:00:00
#SBATCH --error=/home/jhz22/work/_cran_%A_%a.err
#SBATCH --output=/home/jhz22/work/_cran_%A_%a.out
#SBATCH --export ALL

. /etc/profile.d/modules.sh
module purge
module load rhel8/default-icl

export TMPDIR=/rds/user/jhz22/hpc-work/work

module load ceuadmin/R

Rscript -e 'install.packages("paws.analytics")'

    ↩