Setup of modules

  • Location at CSD3: /usr/local/Cluster-Apps/ceuadmin
  • Module files: /usr/local/Cluster-Config/modulefiles/ceuadmin

Recent modules

All entries are ordered chronologically.

Date Add ons Category
2022-10-21 pspp/1.6.0 Generic
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 Genetics1
"" regenie/3.2.1 Genetics
"" GEMMA/0.98.5 Genetics2
"" htslib/1.12 Genetics
"" fcGENE/1.0.7 Genetics3
"" SMR/1.0.3 Genetics
"" FastQTL/2.165 Genetics
"" GitKraken/8.1.0 Generic
2022-10-24 Typora/0.11.8beta Generic
"" pandoc/2.19.2 Generic
"" citeproc/0.4.0.1 Generic
"" citeproc/0.8.0.2 Generic
2022-10-26 circos/0.69-9 Genetics
"" DjVuLibre/3.5.27.1-14 Generic
"" ghostscript/9.56.1 Generic
"" bgen/1.1.7 Genetics
2022-10-27 sqlite/3.39.4 Generic
2022-10-28 poppler/0.84.0 Generic
"" jq/1.6 Generic4
"" DosageConverter/1.0.0 Genetics
"" tidy/5.8.0 Generic
2022-10-29 ghc/8.6.5 Generic
"" pandoc-citeproc/0.17.0.2 Generic
2022-10-31 git/2.38.1 Generic
"" aria2/1.36.0 Generic
2022-11-01 alpine/2.26 Generic
"" readline/8.0 Generic
"" Cytoscape/3.9.1 Generic
"" nano/6.0 Generic
"" R/4.2.2 Generic
"" parallel/20220222 Generic
"" pdf2djvu/0.9.19 Generic
2022-11-02 lapack/3.10.1 Generic
"" GraphicsMagick/1.3.38 Generic
"" QTLtools/1.3.1-25 Genetics5
"" NLopt/2.7.1 Generic
"" blat/37x1 Genetics
"" bedtools2/2.29.2 Genetics
"" bedops/2.4.41 Genetics
2022-11-03 Beagle/3.0.4 Genetics
"" netbeans/15 Generic
"" JAGS/4.3.1 Generic
"" exiv2/0.27.5 Generic6
"" googletest/1.8.0 Generic
"" googletest/1.12.1 Generic
"" libiconv/1.17 Generic
"" ldc2/1.24.0 Generic
"" gettext/0.21 Generic
"" ssw/0.7 Generic
"" fribidi/1.0.8 Generic
"" proj/6.3.0 Generic
"" gmp/6.2.1 Generic
"" pcre2/10.30 Generic
"" zstd/1.5.2 Generic
2022-11-04 libxslt/1.1.34 Generic7
"" libssh2/1.10.0 Generic
"" libxml2/2.9.10 Generic8
"" libsodium/1.10.0 Generic
"" gdal/3.0.4 Generic9
"" expat/2.4.7 Generic10
"" docbook2X/0.8.8 Generic
"" libntlm/1.6 Generic
"" vala/0.46.5 Generic
"" gtksourceview/4.0.3 Generic
"" oniguruma/6.9.8 Generic
"" nspr/4.35 Generic
"" nettle/2.7.1 Generic
2022-11-05 trinculo/0.96 Generic
"" ruby/2.7.5 Generic11
2022-11-06 libpng/0.5.30 Generic
"" libgit2/1.1.0 Generic12
"" git-extras/6.5.0 Generic
"" trousers/0.3.14 Generic
"" libidn2/2.3.4 Generic
"" unbound/1.17.0 Generic
"" nettle/3.6.0 Generic13
"" gnutls/3.7.8 Generic14
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
"" fossil/2.19 Generic
2022-11-10 rclone/1.53.1 Generic
"" 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 Genetics15
"" CAVIARBF/0.2.1 Genetics
2022-11-11 PAINTOR/3.0 Genetics
"" ABCtoolbox/2.0 Generic
"" cppunit/1.15.2 Generic
2022-11-12 ccal/2.5.3 Generic
2022-11-13 axel/2.17.11 Generic16
"" axel/1.0a Generic
"" bazel/2.0.0 Generic
"" bazel/1.2.1 Generic
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
2022-11-18 ffmpeg/5.1.1 Generic
2022-11-19 ensembl-vep/104 Genetics*
"" OpenMS/3.0.0-pre-develop Genetics*17
"" 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*18
"" DEPICT/v1_rel194 Genetics*
"" MAGMA/1.10 Genetics*
"" Pascal/v_debut Genetics*
"" VEGAS2/2.01.17 Genetics*
"" fgwas/0.3.6 Genetics*
2022-11-24 qtcreator/2.5.2 Generic
"" rstudio/2022.07.2+576 Generic
2022-11-26 yaml-cpp/0.7.0 Generic
"" libglvnd/1.6.0 Generic
"" GreenAlgorithmsforHPC/0.2.2-beta Generic
2022-11-28 openssl/1.1.1s Generic
2022-11-29 qt/5.15.7 Generic*
2022-12-02 rstudio/1.3.1093 Generic19
2022-12-04 phenoscanner/v2 Genetics*
2022-12-07 SurvivalAnalysis/2016-05-09 Genetics
2022-12-14 node/16.14.0 Generic
2022-12-19 rstudio/2022.12.0+353 Generic
"" icu/50.2 Generic
2022-12-20 snakemake/7.19.1 Generic
2022-12-21 icu/70.1 Generic
"" libuv/1.43.0 Generic
"" libcares/1.18.1 Generic
"" brotli/1.0.9 Generic
2022-12-28 ncurses/6.3 Generic
2023-01-03 Eagle/2.4.1 Genetics
2023-01-05 GEM/1.4.5 Genetics
2023-02-01 GENEHUNTER/2.1_r6 Genetics
2023-02-26 JabRef/5.9 Generic
2023-02-27 Zotero/6.0.22 Generic
2023-03-14 regenie/3.2.5 Genetics
2023-03-22 rstudio/2023.03.0+386 Generic
2023-03-24 PoGo/1.0.0 Genetics
2023-03-31 PWCoCo/2023-03-31 Genetics20
2023-04-02 regenie/3.2.5.3 Genetics
2023-04-04 PWCoCo/1.0 Genetics
2023-04-05 PhySO/1.0-dev0 Generic
2023-04-21 ImageJ/1.53t Generic
2023-04-25 busybox/1.35.0 Generic
2023-06-02 regenie/3.2.7 Genetics21
2023-06-05 gsl/2.7.1 Generic
2023-06-06 allegre/2.0f Genetics
2023-06-14 autoconf/2.72c.24-8e728 Generic22
2023-06-16 globusconnectpersonal/3.2.2 Generic
2023-06-19 plink-ng/2.00a3.3 Genetics
2023-06-26 RHHsoftware/0.1 Genetics
2023-07-19 pdfjam/3.06 Generic
2023-07-22 rstudio/2023.06.1+524 Generic
2023-07-28 PWCoCo/1.1 Genetics
2023-08-02 regenie/3.2.9 Genetics
"" fossil/2.22 Generic
2023-08-04 quarto/1.3.450-icelake Generic23
2023-08-06 finemap/1.4.2 Genetics
2023-08-10 GreenAlgorithmsforHPC/0.3 Generic
2023-08-12 xpdf/4.04 Generic24
2023-08-22 thunderbird/115.1.1 Generic
2023-08-24 pdfjam/3.07 Generic
2023-09-03 2.0.0-pre1ge32bec Genetic25
"" spead-sheet-widget Generic
2023-09-27 ncbi-vdb/3.0.8 Genetics26
"" sra-tools/3.0.8 Genetics27
"" gatk/4.4.0.0 Genetics28
2023-09-28 openjdk/8u382-b05 Generic
"" openjdk/11.0.20+8 Generic
"" openjdk/17.0.8+7 Generic
2023-10-24 rst2pdf/0.101 Generic
"" geany/1.38 Generic
"" pango/1.41.1 Generic
"" gettext/0.20 Generic
2023-10-26 glib/2.58.3 Generic
2023-10-27 graphene/1.4.0 Generic
"" graphene/1.8.0 Generic
2023-10-24 gtk+/3.24.0 Generic
"" geany/2.0 Generic
2023-10-28 hunspell/1.7.0 Generic
"" hunspell/1.7.2 Generic
"" enchant/2.2.0 Generic
2023-10-29 gtk+/3.90.0 Generic
2023-10-31 vte/0.55.0 Generic
2023-11-05 Anaconda3/2023.09-0 Generic
2023-11-23 SciKit-LLM & OpenAI API Genetic
2023-11-24 ldsc/1.0.1 Genetics
2023-11-30 gdc/1.6.1-1.0.0 Genetics29
2023-12-13 rust/1.74.1 Generic
2023-12-20 verifyBamID/1.1.3 Genetics
2023-12-21 verifyBamID/2.0.1 Genetics30
2023-12-27 regtools/1.0.0 Genetics31
"" VarScan/2.4.6 Genetics32
2024-01-02 Mango/0.1.0 Generic
2024-01-08 picard/3.1.1 Genetics
"" plink/2.0_20240105 Genetics
2024-01-10 cmake/3.28.1 Generic
"" tatami/2.1.2 Generic33
2024-01-19 htslib/1.19 Genetics
2024-01-23 nextflow/23.10.1 Generic34
"" go/1.21.6 Generic
"" singularity/4.0.3 Generic35
"" libseccomp/2.5.5 Generic
2024-01-24 fraposa_pgsc/0.1.0 Genetics36
"" pgsc_calc/2.0.0-alpha.4 Genetics37
2024-01-27 glibc/2.18 Generic
"" glibc/2.26 Generic
"" deno/1.40.2 Generic38
"" deno/1.40.2-icelake Generic
"" quarto/1.4.549 Generic
2024-02-29 R/4.3.3 Generic39
2024-03-01 glpk/5.0 Generic
2024-03-02 glpk/4.57 Generic
2024-03-04 rstudio/2023.12.1-402 Generic
2024-03-05 GitKraken/9.12.0 Generic40
"" automake/1.16.5 Generic41
"" pspp/2.0.0 Generic
2024-03-09 Scala/3.3.3 Generic
2024-03-10 fpc/3.2.2 Generic
"" Swift/5.10 Generic
"" pulsar/1.114.0 Generic
"" VSCodium/1.87.1.24068 Generic
2024-03-27 openssl/3.2.1-icelake Generic42
"" openssh/9.7p1-icelake Generic43
2024-03-31 ensembl-vep/111-icelake Genetics44
2024-04-01 json-c/0.17-20230812-icelake Generic45
"" device-mapper/1.02.28-icelake Generic
"" LVM2/2.03.23-icelake Generic46
2024-04-02 cryptsetup/2.7.1-icelake Generic47
2024-04-05 krb5/1.21.2-icelake Generic48
"" git/1.44.0-icelake Generic49
"" openssl/1.1.1b-icelake Generic
"" libssh2/1.11.0-icelake Generic
"" libssh/0.10.6-icelake Generic
2024-04-22 peer/1.3 Generic50
2024-04-29 ImageMagick/7.1.1-31 Generic51
2024-05-15 rtmpdump/2.3 Generic52
2024-05-22 spyder/5.5.4 Generic53
2024-06-04 pwiz/3_0_24156_80747de Proteomics
2024-06-09 crux/4.2 Proteomics54
"" p7zip-zstd/17.05 Generic55
"" DIA-NN/1.8.1 Proteomics
2024-06-10 patchelf/0.18.0 Generic
"" boost/1.76.0 Generic56
"" wine/8.21 Generic57
2024-06-11 crux/4.1 Proteomics
"" pwiz/3_0_24163_9bfa69a-wine Proteomics
2024-06-13 seqkit/2.8.2 Proteomics58
"" dotnet/8.0.304 Generic
"" dotnet/6.0.423 Generic59
"" FlashLFQ/1.2.6 Proteomics60
"" MetaMorpheus/1.0.5 Proteomics
2024-06-14 R/4.4.1 Generic
2024-06-25 msms/3.2rc-b163 Genetics
2024-06-30 freesurfer/7.4.1 Generic
2024-07-04 docker/24.0.5 Generic61
"" docker/27.0.3 Generic
2024-07-05 sshpass/1.10 Generic
"" podman/5.1.1 Generic62
2024-07-09 ntlm/1.6 Generic
"" alpine/2.26-icelake Generic63
"" gnutls/3.8.4-icelake Generic
"" quarto/1.6.1-icelake Generic
"" gettext/0.22.5-icelake Generic
"" nettle/3.9-icelake Generic
2024-07-11 qemu/9.0.1 Generic64
2024-07-13 msamanda/3.0.21.532 Proteomics
2024-07-16 augeas/1.14.1 Generic
"" hivex/1.3.23 Generic65
"" ocaml/4.14.2 Generic
"" findlib/1.9.6 Generic66
"" opam/2.2.0 Generic67
"" libguestfs/1.48.6 Generic68
2024-07-23 Miniconda3/22.9.0 Generic
2024-07-25 pigz/2.8 Generic
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 Proteomics69
2024-08-14 ThermoRawFileParser/1.4.4 Proteomics
"" ThermoRawFileParserGUI/1.7.4 Proteomics
"" FragPipe/22.0 Proteomics70
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
2024-08-23 qpdf/11.9.1 Generic
2024-09-01 MaxQuant/2.6.4.0 Proteomics
"" Perseus/2.1.2.0 Proteomics
2024-09-03 tiff/4.0.4 Generic
"" tiff/4.6.0 Generic
2024-09-05 libgit2/1.4.2 Generic
2024-09-10 jasper/4.2.4 Generic71
2024-09-13 geos/3.8.4 Generic
"" prof/7.2.1 Generic
2024-09-14 libarchive/3.7.5 Generic
"" openssl/3.2.1 Generic
"" curl/7.85.0 Generic72
2024-09-15 libjpeg-turbo/3.0.4 Genetic73
"" libgeotiff/1.7.3 Generic74
"" gdal/3.7.0 Generic75
2024-10-04 libsodium/1.0.20 Genetic
"" SYMPHONY/3.6.17 Generic
2024-10-13 sage/0.14.7 Proteomics
2024-10-23 caddy/2.7.5 Genetic
"" caddy/2.8.4 Generic
"" nginx/1.24.0 Generic
"" wrk/4.2.0 Generic
2024-10-25 firefox/131.0.3 Genetic
"" chromium/132.0.6798.0 Generic
2024-10-29 inetutils/2.5 Genetic76
2024-10-31 R/4.4.2 Generic
2024-11-01 edge/130.0.2849.56-1 Generic
2024-11-22 pspp/2.0.1 Generic
2024-11-26 pgsc_calc/2.0.0 Generic
2024-12-03 firefox/133.0 Genetic
2024-12-07 firefox/nightly Genetic
2024-12-10 rstudio/2024.09.1+394 Genetic
2025-01-21 node/18.20.5 Genetic77
2025-01-26 node/20.18.2 Generic
"" chrome/132.0.6834.110 Generic78
2025-01-29 brotli/1.1.0 Generic79
2025-01-31 rust/1.84.1 Generic80
2025-02-04 quarto/1.7.13 Generic
"" pandoc/3.6.2 Generic
2025-02-05 rstudio/2025.04.0+278 Genetic
"" git/2.48.1 Generic81
"" libgcrypt/1.5.3 Generic82
"" texinfo/7.2 Generic83
2025-02-24 VSCode/1.97.2 Genetic
2025-02-26 ollama/0.5.12 Genetic84
2025-02-28 R/4.4.3 Generic
2025-03-01 leptonica/1.85.0 Generic
"" tesseract/5.5.0 Generic85
2025-03-02 apidog/latest Generic86
2025-03-03 micromamba/2.0.5 Generic
2025-03-13 DjVuLibre/3.5.28 Generic
"" ollama/0.6.0 Generic
2025-03-16 qt/6.8.2 Generic
"" Anaconda3/2024.10-1 Generic87
2025-03-17 micromamba/2.0.7 Generic88
"" binutils/2.44 Generic
2025-03-18 OpenMS/3.4.0 Proteomics
2025-03-20 ollama/0.6.2 Generic
2025-03-22 diann/2.0.2 Proteomics89
2025-03-25 firefox/60.5.1-1.el7 Generic90
2025-03-26 firefox/136.0 Generic
2025-03-29 llama.cpp/b4991 Generic91
2025-04-05 InstaNovo/1.1.1-GPU Proteomics92
2025-04-07 scGPT/0.2.4 Single cell93
"" scanpy/1.11.1 Single cell94
2025-04-11 R/4.5.0 Generic
"" llama.cpp/b5121 Generic
2025-04-12 ollama/0.6.5 Generic
2025-04-15 DrugAssist/latest Generic95
2025-04-16 uv/0.6.14 Generic96
"" InstaNovo/1.1.1 Proteomics
"" diann/2.1.0 Proteomics
2025-04-17 BitNet/b1.58-2B-4T Generic97
2025-04-19 C2S-Scale/0.0.2 Single cell98
2025-04-20 VSCode/1.99.3 Generic
2025-04-23 gcta/1.94.4 Genetics
2025-04-24 cbindgen/0.28.0 Generic99
"" clang/19.1.7 Generic
"" dump_syms/2.3.4 Generic
"" nasm/2.16.03 Generic
"" node/18.19.0 Generic
"" pkg-config/1.8.0 Generic
2025-04-29 AnythingLLMDesktop/latest Generic
2025-05-02 llama.cpp/b5259 Generic
2025-05-03 GENIE/1.1.1 Genetics100
2025-05-05 ollama/0.6.8 Generic
2025-05-06 SuSiEx/1.1.2 Genetics
2025-05-07 Synapse/4.8.0 Generic
"" llama.cpp/b5305 Generic
2025-05-09 PGS-CSx/1.1.0 Genetics101
2025-05-10 VSCODE/1.100.0 Generic
2025-05-14 RSEM/1.3.3 Genetics102
2025-05-15 BWA/0.7.19 Genetics
2025-05-16 ollama/0.7.0 Generic
2025-05-17 VirtualBox/7.1-7.1.8_168469 Generic103
2025-05-18 VSCODE/1.100.2 Generic
2025-05-19 geany/2.0-icelake Generic
2025-05-20 vdo/8.3.1.1 Generic104
2025-05-22 rust/nightly Generic80
"" edit/1.0.0 Generic105
2025-05-23 Windsurf/1.6.5 Generic
2025-05-25 ollama/0.7.1 Generic
2025-05-29 sqlite/3.49.2 Generic106
2025-05-30 ollama/0.9.0 Generic
2025-06-01 llama.cpp/b5558 Generic91
2025-05-30 ollama/0.9.0 Generic
2025-06-14 edit/1.2.0 Generic
"" VSCode/1.101.0 Generic
"" R/4.5.1-icelake Generic
2025-07-05 Zettlr/3.5.1 Generic107
2025-07-14 edlib/1.2.7 Genetics108
"" MUMmer/4.0.1 Genetics
2025-07-15 SVanalyzer/0.36 Genetics109
2025-07-16 sniffles/2.2 Genetics110
"" awscli/2.27.52 Generic111
"" SEQPower/1.1.0 Genetics112
2025-07-18 truvari/5.3.0 Genetics113
2025-07-19 hap.py/0.3.15 Genetics114
"" rtg-tools/3.13 Genetics115
2025-08-01 ollama/0.10.1 Generic
"" llama.cpp/b6059 Generic
"" fly/0.3.164 Generic116
"" node/22.16.0 Generic
2025-08-03 cli/2.76.2 Generic117
2025-08-05 qctool/2.2.5 Genetics
"" MToolBox/1.2.1 Genetics118
2025-08-08 ollama/0.11.4 Generic
"" VSCode/1.103.0 Genetic119
"" LLM/0.26 Genetic120
"" llama.cpp/b6119 Genetic
"" gsutil/5.35 Generic
"" python/3.12.10 Generic
2025-08-10 haplogrep/2.4.0 Genetics121
"" haplogrep/3.2.2 Genetics
2025-08-11 flashpca/2.0 Genetics122
2025-08-13 fNUMT/1.1 Genetics123
"" NUMTFinder/0.5.5 Genetics
"" simNGS/1.7 Genetics124
2025-08-18 Anaconda2/2.5.0 Generic
"" impute5/1.2.0 Genetics
"" shapeit5/5.1.1 Genetics
2025-08-20 snakemake/9.9.0 Generic

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

Three aspects are notable,

  1. A file named NOTE indicates the original annotation.
  2. A symbolic link is generated when appropriate to simplify executable file name.
  3. The available source package is kept in the sources/ directory.

Word cloud diagrams

They are generated from script setup.sh,

Footnotes


  1. metal

    Notes on METAL 2020-05-05r

    This version has options EFFECT_PRINT_PRECISION and STDERR_PRINT_PRECISION (both with default 4) to enable many decimal places.

    The letter r as in 2020-05-05r indicates a replacement of functions in libsrc/MathStats.cpp to ensure generality – details have also been posted to the GitHub page, https://github.com/statgen/METAL/issues/24.

    FATAL ERROR -
    a too large, ITMAX too small in gamma countinued fraction (gcf)
    
    so the -1.info file could not be generated.
    

  2. gemma

    Note on compiling from source

    A considerably smaller (1,097,256 vs 22,721,624) executable, /usr/local/Cluster-Apps/ceuadmin/GEMMA/0.98.5/bin, is generated under CSD3 but the original distribution is used by default.

    module load openblas/0.2.15
    make
    

  3. fcgene

    Alternative site

    See https://github.com/dr-roshyara/fcgene 

  4. jq

    The executable points to the one available from the website.

    The bin/, include/, lib/, share/ directories are obtained from source with oniguruma also compiled independently. 

  5. qtltools

    The long version number is 1.3.1-25-g6e49f85f20. 

  6. exiv2

    This is compiled with configuration

    cmake -DCMAKE_INSTALL_PREFIX=$CEUADMIN/exiv/0.27.5 -DEXIV2_ENABLE_NLS=On -DEXIV2_ENABLE_BMFF=On -DEXIV2_BUILD_UNIT_TESTS=Off -DCMAKE_PREFIX_PATH=$HPC_WORK ..
    

    The modules ceuadmin/gettext/0.21, ceuadmin/libiconv/1.17, ceuadmin/googletest/1.8.0 are at disposal. 

  7. libxslt

    There is complaint about docbook as in expat, however there is no apparent option to control for this. 

  8. libxml2

    The packaging is not perfect and Python 2 package requires to be manually furnished,

    export PYTHONPATH=/usr/local/Cluster-Apps/ceuadmin/libxml2/2.9.10/lib/python2.7/site-packages
    ./configure --prefix=$CEUADMIN/libxml2/2.9.10
    cd libxml2-2.9.10/python
    python setup.py install --prefix=${PYTHONPATH}
    

    The module file is expicitly appended with

    module load python/2.7
    export PYTHONPATH=$root/lib/python2.7/site-packages:$PYTHONPATH
    

  9. gdal

    This involves many libraries; an expeeriment has been done as follows,

    module load gcc/6
    module load cfitsio-3.450-gcc-5.4.0-colpo6h
    module load geos-3.6.2-gcc-5.4.0-vejexvy
    module load jpeg-9b-gcc-5.4.0-7s6bvoe
    module load libgeotiff-1.4.2-gcc-5.4.0-2emzhxh
    module load libpng-1.6.29-gcc-5.4.0-3qwhidp
    module load mpich-3.2-gcc-5.4.0-idlluti
    module load netcdf/4.4.1
    module load postgresql-9.5.3-gcc-5.4.0-fxmot7h
    module load zlib/1.2.11
    module load zstd-1.3.0-intel-17.0.4-eyn6gaw
    ./configure --with-libjson-c=$HPC_WORK --with-proj=$HPC_WORK --without-sqlite3 --prefix=$HPC_WORK \
      --with-cfitsio=/usr/local/software/spack/current/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/cfitsio-3.450-colpo6hwycaaind2al47yriydf4oysyx \
      --with-cpp14
    # module load json-c-0.13.1-gcc-5.4.0-ffamohj
    # module load proj-6.2.0-gcc-5.4.0-iw4jbzs
    # --with-proj=/usr/local/software/spack/spack-git/opt/spack/linux-rhel7-broadwell/gcc-5.4.0/proj-6.2.0-iw4jbzsrjirypecjm4c7bmlhdvhgwjmx \
    

    On icelake, this is updated as follows,

    module load ceuadmin/proj/6.3.0
    module load ceuadmin/jasper/4.2.4
    module load libxml2/2.9.13/gcc/fww2yzpt
    module load ceuadmin/json-c/0.17-20230812-icelake
    wget -qO- https://github.com/OSGeo/gdal/archive/refs/tags/v3.0.4.tar.gz | \
    tar xvfz -
    cd gdal-3.0.4/gdal
    ./configure --prefix=$CEUADMIN/gdal/3.0.4 --with-libjson-c=$CEUADMIN/json-c/0.17-20230812-icelake \
                --with-proj=/usr/local/Cluster-Apps/ceuadmin/proj/6.3.0 \
                --without-sqlite3
    make
    

  10. expat

    Due to error messages, the options are specified as follows,

    ./configure --prefix=$CEUADMIN/expat/2.4.7 --without-docbook
    

  11. ruby

    This is done as follows,

    curl -sSL https://cache.ruby-lang.org/pub/ruby/2.7/ruby-2.7.5.tar.gz -o ruby-2.7.5.tar.gz
    tar -xzf ruby-2.7.5.tar.gz
    cd ruby-2.7.5
    ./configure --prefix=$CEUADMIN/ruby/2.7.5
    make
    make install
    rvm reset
    

  12. libgit2

    It uses Python 2.7 and libssh2 (as above). The following warnings are given

    /usr/bin/ld: warning: libssl.so.10, needed by /home/jhz22/hpc-work/lib/libssh2.so, may conflict with libssl.so.1.1
    /usr/bin/ld: warning: libcrypto.so.10, needed by /home/jhz22/hpc-work/lib/libssh2.so, may conflict with libcrypto.so.1.1
    

  13. nettle

    This is required by gnutls/3.7.8, which requires ceuadmin/gmp/6.2.1 and --enable-mini-gmp.

    Alternatively, we use

    ./configure --prefix=$HPC_WORK LDFLAGS=-L$HPC_WORK/lib64 LIBS=-lhogweed --disable-openssl \
                --with-lib-path=/usr/local/Cluster-Apps/ceuadmin/gmp/6.2.1/lib \
                --with-include-path=/usr/local/Cluster-Apps/ceuadmin/gmp/6.2.1/include
    

  14. gnutls

    It requires libunistring (optionally –with-included-unistring), libidn2, libunbound, and trousers, all prepared above.

    ./configure --prefix=$HPC_WORK --with-included-unistring --with-nettle-mini --enable-ssl3-support \
                CFLAGS=-I$HPC_WORK/include LDFLAGS=-L$HPC_WORK/lib LIBS=-lhogweed LIBS=-lunbound LIBS=-ltspi \
                --enable-sha1-support --disable-guile
    

    It is necessary to edit lib/pkcs11_privkey.c to make ck_rsa_pkcs_pss_params definition explicit. Then there is error with guile so we use –disable-guile.

    Under icelake (CentOS 8), this configuration is used for gnutls/3.8.4-icelake,

    module load gettext/0.21/gcc/qnrcglqo
    configure --prefix=$CEUADMIN/gnutls/3.8.4-icelake --with-included-unistring
    make
    make install
    

  15. lemma

    The documentation indicates a requirement of gcc/9.4, boost/1.78, OpenMP/3.1 and/or Intel MKL Library 2019 Update 1 but it is possible to proceed with gcc/11, cmake-3.19.7-gcc-5.4-5gbsejo, boost-1.66.0-gcc-5.4.0-slpq3un, ceuadmin/bgen. 

  16. The following scripts avoid option --without-ssl.

     wget -qO- https://github.com/axel-download-accelerator/axel/releases/download/v2.17.11/axel-2.17.11.tar.gz | \
     tar xvfz -
     cd axel-2.17.11
    ./configure --prefix=$CEUADMIN/axel/2.17.11  LDFLAGS=-L/usr/lib64 LIBS=-lssl
    

  17. OpenMS

    When the OpenMS module is loaded, pyopenms and alphapept also become available. 

  18. locuszoom

    The version adds chromosome X data and will have options using INTERVAL data. 

  19. rstudio

    This is replacement of the module by HPC (no longer working) with the RStudio itself unchanged.

    To save space, 2023.06.1+524 is removed upon installation of 2023.12.1+402. 

  20. pwcoco

    It compiles under gcc/9. Upon release of 1.1, this snapshot is removed. 

  21. regenie

    cd ~/rds/public_databases/software/
    wget -qO- https://github.com/rgcgithub/regenie/archive/refs/tags/v3.2.7.tar.gz | \
    tar xvfz -
    cd regenie-3.2.7/
    export BGEN_PATH=~/rds/public_databases/software/bgen
    module load zlib/1.2.11
    export ZLIB_LIBRARY=/usr/local/Cluster-Apps/zlib/1.2.11
    module load gcc/6
    module load cmake-3.19.7-gcc-5.4-5gbsejo
    module load intel/mkl/mic/2018.4
    mkdir build
    cd build
    cmake ..
    make
    

  22. autoconf

    git clone git://git.sv.gnu.org/autoconf
    cd autoconf/
    ./bootstrap
    module load help2man-1.47.4-gcc-4.8.5-phopsy7
    ./configure --prefix=/home/jhz22/rds/public_databases/software
    moke
    make install
    

  23. quarto

    See https://cambridge-ceu.github.io/csd3/applications/quarto.html

  24. xpdf

    To enable display fonts as in login-e-[1-4] in /etc/xpdfrc or ~/.xpdfrc

    # SJR addition
    fontFile Times-Roman           /usr/share/fonts/urw-base35/NimbusRoman-Regular.t1
    fontFile Times-Italic          /usr/share/fonts/urw-base35/NimbusRoman-Italic.t1
    fontFile Times-Bold            /usr/share/fonts/urw-base35/NimbusRoman-Bold.t1
    fontFile Times-BoldItalic      /usr/share/fonts/urw-base35/NimbusRoman-BoldItalic.t1
    fontFile Helvetica             /usr/share/fonts/urw-base35/NimbusSans-Regular.t1
    fontFile Helvetica-Oblique     /usr/share/fonts/urw-base35/NimbusSans-Italic.t1
    fontFile Helvetica-Bold        /usr/share/fonts/urw-base35/NimbusSans-Bold.t1
    fontFile Helvetica-BoldOblique /usr/share/fonts/urw-base35/NimbusSans-BoldItalic.t1
    fontFile Courier               /usr/share/fonts/urw-base35/NimbusMonoPS-Regular.t1
    fontFile Courier-Oblique       /usr/share/fonts/urw-base35/NimbusMonoPS-Italic.t1
    fontFile Courier-Bold          /usr/share/fonts/urw-base35/NimbusMonoPS-Bold.t1
    fontFile Courier-BoldOblique   /usr/share/fonts/urw-base35/NimbusMonoPS-BoldItalic.t1
    fontFile Symbol                /usr/share/fonts/urw-base35/StandardSymbolsPS.t1
    fontFile ZapfDingbats          /usr/share/fonts/urw-base35/D050000L.t1
    

  25. pspp

    See https://cambridge-ceu.github.io/csd3/applications/pspp.html.

    Makeinfo

    The following replacement is used.

    MAKEINFO = ${SHELL} '/rds/project/jmmh2/rds-jmmh2-public_databases/software/pspp-2.0.0-pre1ge32bec/build-aux/missing' makeinfo --force --no-validate
    

    while the rest is copied from GNU build, https://benpfaff.org/~blp/pspp-master/20230624103130/x86_64/pspp-2.0.0-pre1ge32bec-x86_64-build20230624103419.tar.gz

  26. ncbi-vdb

    The installation is preceeded with module load gcc/6 flex-2.6.4-gcc-5.4.0-2u2fgon. Although configure is provided, cmake is used instead.

    cmake -DCMAKE_PREFIX_PATH=$CEUADMIN/ncbi-vdb/3.0.8 -DCMAKE_INSTALL_PREFIX=$CEUADMIN/ncbi-vdb/3.0.8 ..
    

  27. sra-tools

    First, create a symbolic link for ncbi-vdb/3.0.8 in the parent directory.

    cmake -DVDB_LIBDIR=$CEUADMIN/ncbi-vdb/3.0.8/lib64 -DCMAKE_INSTALL_PREFIX=$CEUADMIN/sra-tools/3.0.8 ..
    

    Drop constexpr as in constexpr size_type max_size() const { return SIZE_MAX; } in line 161 of the following header file:

    /usr/local/Cluster-Apps/ceuadmin/sra-tools/3.0.8/tools/external/driver-tool/util.hpp

  28. gatk

    The Python dependencies are set up as follows,

    module load anaconda/3.2019-10
    conda env create -p /usr/local/Cluster-Apps/ceuadmin/gatk/4.4.0.0/anaconda-3.2019-10 -f gatkcondaenv.yml
    conda activate /usr/local/Cluster-Apps/ceuadmin/gatk/4.4.0.0/anaconda-3.2019-10
    

    Workflow downloads: https://github.com/gatk-workflows 

  29. gdc

    It also includes gdc_dtt-ui 1.0.0 

  30. VB2

    To build from source, module htslib-1.9-gcc-5.4.0-p2taavl is needed yet with message /usr/bin/ld: warning: libbz2.so.1.0, needed by /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/htslib-1.9-p2taavlu3ieppo25otjfgvfu5tysbgho/lib/libhts.so, may conflict with libbz2.so.1. In fact, 1 == 1.0 so it is ignored. 

  31. regtools

    gcc/6 is required for C++11. 

  32. varscan

    Simply call java -jar $VARSCAN_HOME/VarScan.v2.4.6.jar after module load ceuadmin/VarScan/2.4.6

  33. tatami

    The following aspects are required.

    1. module load gcc/9
    2. mkdir build && cd build
    3. cmake .. -DCMAKE_INSTALL_PREFIX=$CEUADMIN/tatami/2.1.2
    4. cmake –build . –target install

  34. nextflow

    curl -fsSL get.nextflow.io | bash
    

  35. singularity

    The singularity module in place is already very useful, e.g.,

    singularity pull tensorflow_latest_gpu.sif docker://tensorflow/tensorflow:latest-gpu
    singularity build --sandbox tensorflow docker://tensorflow/tensorflow:latest-gpu
    singularity run tensorflow
    python -c '
    from tensorflow.python.client import device_lib
    print(device_lib.list_local_devices())
    '
    

    where we pull the container both in Singularity Image Format (SIF) format and into a directory. However, we now have

    mconfig --prefix=$CEUADMIN/singularity/4.0.3 --without-seccomp --without-conmon --without-suid
    cd builddir & make
    

  36. fraposa

    Several packages, including poetry, poetry-plugin-export and fraposa_pgsc, will be installed as follows,

    module load ceuadmin/Anaconda3/2023.09-0
    pip install poetry
    pip3 install poetry-plugin-export
    pip install --use-feature=fast-deps .
    scripts/run_example.sh
    

    This is necessay since by default peotry install will use user's home directory. As indicated from poetry install --help:

    The install command reads the poetry.lock file from the current directory, processes it, and downloads and installs all the libraries and dependencies outlined in that file. If the file does not exist it will look for pyproject.toml and do the same. 

  37. pgsc_calc

    Application, https://pgsc-calc.readthedocs.io/en/latest/index.html

    nextflow run pgscatalog/pgsc_calc -profile test,singularity
    

    It appears quarto is called so presumably under icelake.

    For 2.0.3, we try the conda option. 

  38. deno

    Web: https://anaconda.org/conda-forge/deno/files

    wget https://anaconda.org/conda-forge/deno/1.40.2/download/linux-64/deno-1.40.2-hfc7925d_0.conda -O deno.conda
    unzip deno.conda
    tar --use-compress-program=unzstd -xvf pkg-deno-1.40.2-hfc7925d_0.tar.zst
    

  39. R

    This replaces R/4.3.2. It is also R/latest. 

  40. GitKraken

    This replaces 8.1.0. 

  41. automake

    This is required by pspp 2.0.0. 

  42. openssl

    Archive, https://www.openssl.org/source/old/

    wget -qO- https://www.openssl.org/source/openssl-3.2.1.tar.gz | \
    tar xvfz -
    cd openssl-3.2.1/
    export PERL5LIB=
    ./Configure --prefix=$CEUADMIN/openssl/3.2.1-icelake --openssldir=$CEUADMIN/openssl/3.2.1-icelake/ssl
    make
    make install
    

    One can check version with openssl version. For 1.1.1b, it is the followiong,

    wget -qO- https://github.com/openssl/openssl/archive/refs/tags/OpenSSL_1_1_1b.tar.gz | \
    tar xvfz -
    cd openssl-OpenSSL_1_1_1b/
    config --prefix=$CEUADMIN/openssl/1.1.1b-icelake --openssldir=$CEUADMIN/openssl/1.1.1b-icelake/ssl
    make install
    

    Module ceuadmin/openssl/3.2.1 actually points to /usr/local/Cluster-Apps/openssl/3.2.1

  43. openssh

    OpenSSL is called first to use the specific openssl, e.g.,

    module load ceuadmin/openssl/3.2.1-icelake
    ./configure --prefix=$CEUADMIN/openssh/9.7p1-icelake --with-ssl-dir=$CEUADMIN/openssl/3.2.1-icelake
    make
    make install
    

    Check is made with cat config.log | grep -i openssl. However, variable EVP_PKEY_bits is nonexistent. It turns out the default ssl is fine.

    configure --prefix=$CEUADMIN/openssh/9.7p1-icelake
    make
    make install
    

    However, EVP_KDF_ctrl is missing with git. 

  44. ensembl-vep

    Note that a nextflow pipeline is now available from nextflow/. A test has been done as follows,

    export PERL5LIB=
    module load ceuadmin/libssh
    git clone https://github.com/Ensembl/ensembl-vep.git
    cd ensembl-vep
    perl INSTALL.pl -l Bio -y GRCh37 -a acfp -g all -s homo_sapiens,homo_sapiens_merged --NO_TEST -c .vep
    ./vep -i examples/homo_sapiens_GRCh38.vcf --cache .vep
    

    A log file is kept here.

    Moreover, we could also add some plugin data, https://github.com/Ensembl/VEP_plugins.

    For the nearest gene, the Set::IntervalTree is required and is furnished as follows,

    cpanm -l /usr/local/Cluster-Apps/ceuadmin/ensembl-vep/111-icelake/Bio ExtUtils::CppGuess
    cpanm -l /usr/local/Cluster-Apps/ceuadmin/ensembl-vep/111-icelake/Bio ExtUtils::CBuilder
    cpanm -l /usr/local/Cluster-Apps/ceuadmin/ensembl-vep/111-icelake/Bio Set::IntervalTree
    

    In general, with perl -MCPAN -e shell we specify

    o conf makepl_arg "PREFIX=/usr/local/Cluster-Apps/ceuadmin/ensembl-vep/111-icelake/Bio" o conf makepl_arg "INSTALL_BASE=/usr/local/Cluster-Apps/ceuadmin/ensembl-vep/111-icelake/Bio" ‘o conf commit'

    to see commit: wrote '/home/jhz22/.cpan/CPAN/MyConfig.pm'. However, this is NOT the case here.

    Our module has PERL5LIB=$root/Bio:$root/Bio/lib/perl5/x86_64-linux-thread-multi/.

    Our example data here is 442807041.vcf,

    ##fileformat=VCFv4.0
    #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
    2	101332618	2:101332618_C_T	T	C	.	.	.
    

    and we run script,

    vep --input_file 442807041.vcf \
        --output_file 442807041.tab --force_overwrite \
        --offline --cache --dir_cache /usr/local/Cluster-Apps/ceuadmin/ensembl-vep/111-icelake/.vep \
        --species homo_sapiens --assembly GRCh37 --pick --nearest symbol --symbol \
        --tab
    

    Further information, https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html

  45. json-c

    export LD_LIBRARY_PATH=
    wget -qO- https://github.com/json-c/json-c/archive/refs/tags/json-c-0.17-20230812.tar.gz | \
    tar xvfz -
    cd json-c-0.17-20230812
    mkdir build && cd build
    cmake -DCMAKE_INSTALL_PREFIX=/usr/local/Cluster-Apps/ceuadmin/json-c/0.17-20230812-icelake ..
    ln -sf /usr/include/locale.h xlocale.h
    make -I.
    make install
    

  46. LVM2

    Only device mapper is installed, i.e.,

    wget -qO-  https://sourceware.org/ftp/lvm2/LVM2.2.03.23.tgz | \
    tar xvfz -
    cd LVM2.2.03.23
    ./configure --prefix=$CEUAMIN/LVM2/2.03.23-icelake --with-vdo=none
    make device-mapper
    make install_device-mapper
    

  47. cryptosetup

    # incomplete libssh in need of a fix
    module load cmake/3.21.3/intel/wce32356
    wget -qO- https://www.libssh.org/files/0.10/libssh-0.10.6.tar.xz | \
    tar xfJ -
    cd libssh-0.10.6
    mkdir build && cd build
    cmake -DCMAKE_INSTALL_PREFIX=$CEUADMIN/libssh/0.10.6-icelake  ..
    make
    module load ceuadmin/json-c/0.17-20230812-icelake
    module load ceuadmin/LVM2/2.03.23-icelake
    module load ceuadmin/popt/1.19-icelake
    module load gettext/0.21/gcc/qnrcglqo
    CFLAGS="-I/usr/local/Cluster-Apps/ceuadmin/LVM2/2.03.23-icelake/include" \
    configure --prefix=$CEUADMIN/cryptsetup/2.7.1-icelake --disable-ssh-token
    

  48. krb5-icelake

    It is possible to use the default ssh.

    configure --prefix=$CEUADMIN/krb5/1.21.2-icelake
    module load gettext/0.21/gcc/qnrcglqo
    make install
    

  49. git-2.44.0-icelake

    wget -qO- https://github.com/git/git/archive/refs/tags/v2.44.0.tar.gz | \
    tar xvfz -
    cd git-2.44.0
    make configure
    configure --prefix=${CEUADMIN}/git/2.44.0-icelake
    make
    make install
    

    There remains an error message git-remote-https: symbol lookup error: /usr/lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b

  50. peer

    This is documented separately in the R section, https://cambridge-ceu.github.io/csd3/applications/peer.html

  51. ImageMagick

    wget -qO- https://github.com/ImageMagick/ImageMagick/archive/refs/tags/7.1.1-31.tar.gz | \
    tar xvfz -
    cd ImageMagick-7.1.1-31/
    ./configure --prefix=$CEUADMIN/ImageMagick/7.1.1-31
    make
    make install
    

  52. rtmpdump

    It is necessary for RCurl 1.98-1.14. With curl-7.63.0-gcc-5.4.0-4uswlql we could also install rtracklayer 1.64.0.

    wget -qO- https://rtmpdump.mplayerhq.hu/download/rtmpdump-2.3.tgz |\
    tar xvfz -
    cd rtmpdump-2.3
    sed -i 's|/usr/local|/usr/local/Cluster-Apps/ceuadmin/rtmpdump/2.3|' Makefile
    sed -i 's|/usr/local|/usr/local/Cluster-Apps/ceuadmin/rtmpdump/2.3|' librtmp/Makefile
    make
    make install
    Rscript -e 'install.packages("RCurl")'
    Rscript -e 'BiocManager::install("rtracklayer")'
    

  53. spyder

    cd /rds/project/jmmh2/rds-jmmh2-public_databases/software
    wget https://github.com/spyder-ide/spyder/releases/download/v5.5.4/EXPERIMENTAL-Spyder-5.5.4-Linux-x86_64.sh
    bash EXPERIMENTAL-Spyder-5.5.4-Linux-x86_64.sh
    

  54. crux

    See https://cambridge-ceu.github.io/csd3/applications/crux.html

  55. p7zip-zstd

    A simple make is sufficient but it is necessary to implement a minor revision of install.sh, line 19, so that DEST_HOME=/usr/local/Cluster-Apps/ceuadmin/p7zip-zstd/17.05

  56. boost

    module load python/3.8.11/gcc/pqdmnzmw
    wget -qO- http://sourceforge.net/projects/boost/files/boost/1.76.0/boost_1_76_0.tar.gz | \
    tar xvzf -
    cd boost_1_76_0
    ./bootstrap.sh
    ./b2 --prefix=$CEUADMIN/boost/1.76.0 install
    ./bjam --with-regex --with-filesystem --with-iostreams --with-thread --with-program_options \
            --with-serialization --with-system --with-date_time install
    export BOOST_ROOT=/usr/local/src/boost_1_76_0
    

  57. wine

    module load ceuadmin/krb5/1.21.2-icelake
    configure --prefix=${CEUADMIN}/wine/8.21 --enable-win64
    make install
    

  58. seqkit

    An attempt is made with UniProt, current_release/uniref/uniref100/, knowledgebase/genome_annotation_tracks/UP000005640_9606_beds.

    #!/usr/bin/bash
    
    export fasta=~/rds/public_databases/UniProt/uniref100.fasta.gz
    export fasta=~/rds/public_databases/UniProt/uniprot_sprot.fasta.gz
    export regions=UP000005640_9606_proteome.bed
    
    module load ceuadmin/seqkit
    seqkit subseq --bed ${regions} --seq-type protein --out-file output.fasta ${fasta}
    
    awk '{print $4}' ${regions} | sort | uniq > protein_ids.txt
    seqkit grep -f protein_ids.txt ${fasta} > output.fasta
    
    # A contrast with the genomic counterpart
    # bedtools getfasta -fo output.fasta -s -fullHeader -fi ${fasta} -bed ${regions}
    

  59. dotnet

    The paket tool is installed as follows,

    cd /usr/local/Cluster-Apps/ceuadmin/dotnet/6.0.423
    dotnet new tool-manifest
    dotnet tool install paket
    dotnet paket
    dotnet paket add Mono.Unix --version 7.1.0-final.1.21458.1
    ```
    
    The last line above is for OpenMS. We see `.config/dotnet-tools.json` and also
    
    ```
    Paket version 8.0.3+75b30cdcb8859e8d129f139444d9b9b600bfff07
    Adding package 'Mono.Unix' 7.1.0-final.1.21458.1
    Resolving dependency graph...
     - Mono.Unix is pinned to 7.1.0-final.1.21458.1
    Updated packages:
      Group: Main
        - Mono.Unix: 7.1.0-final.1.21458.1 (added)
    Created dependency graph (1 packages in total)
    Downloading Mono.Unix 7.1.0-final.1.21458.1
    Download of Mono.Unix 7.1.0-final.1.21458.1 done in 249 milliseconds. (231504 kbit/s, 6 MB)
     - Project GenerateDeps.proj needs to be restored
    Resolved package 'Mono.Unix' to version 7.1.0-final.1.21458.1
    Total time taken: 3 seconds
    ```
    
    

  60. FlashLFQ

    Web: https://github.com/smith-chem-wisc/FlashLFQ/wiki/Using-the-Command-Line

    In the script below, a benchmark provided by the software available from ${FLASHLFQ_ROOT}/src/Test/SampleFiles.

    module load ceuadmin/FlashLFQ
    flashlfq --idt MaxQuant/msms.txt --rep . --ppm 5 --chg
    

    which works on MaxQuant/msms.txt and generates FlashLfqSettings.toml, QuantifiedPeaks.tsv, QuantifiedPeptides.tsv and QuantifiedProteins.tsv

  61. docker

    See https://cambridge-ceu.github.io/csd3/applications/docker.html

  62. podman

    See https://cambridge-ceu.github.io/csd3/applications/podman.html

  63. alpine

    Module ceuadmin/alpine/2.26-icelake compiled using gcc/11.2.0/gcc/rjvgspag

  64. qemu

    See https://cambridge-ceu.github.io/csd3/applications/qemu.html

  65. hivex

    wget -qO- https://download.libguestfs.org/hivex/hivex-1.3.23.tar.gz | tar xfz -
    cd hivex-1.3.23
    module load ceuadmin/ocaml/4.14.2
    module load ceuadmin/ruby/2.7.5
    export PERLB5LIB=
    autoreconf -i --force
    ./generator/generator.ml
    ./configure --prefix=$CEUADMIN/hivex/1.3.23
    make
    cd perl
    perl Makefile.PL INSTALLDIRS=site INSTALL_BASE=/usr/local/Cluster-Apps/ceuadmin/hivex/1.3.23
    cd ..
    make
    make install
    

    The release version has hivex.h but GitHub releases doesn't; however since ocaml is available it can be generated from generator/generator.ml.. The INSTALL_PREFIX is replaced with INSTALL_BASE. Moreover, ocaml, Perl and ruby are enabled. Due to permission issue, Python binding is not enabled.

    /usr/bin/install: cannot create regular file '/usr/local/software/spack/spack-views/._rhel8-icelake-20211027_2/uxqqj4xcjrltatqgtuoi2hp46uabtzom/python-3.8.11/gcc-11.2.0/pqdmnzmwkrtp4e3gjibmcxho7g6ekpat/lib/python3.8/site-packages/libhivexmod.cpython-38-x86_64-linux-gnu.so': Permission denied
    

  66. findlib

    wget -qO- http://download.camlcity.org/download/findlib-1.9.6.tar.gz | tar xfz -
    cd findlib-1.9.6
    configure -bindir $CEUADMIN/findlib/1.9.6/bin -mandir $CEUADMIN/findlib/1.9.6/man
    make
    make install
    

  67. opam

    opam init
    opam switch list
    opam switch list-available
    opam switch create ocaml-4.14
    opam install -y hivex --destdir $CEUADMIN/hivex/1.3.23
    

  68. libguestfs

    wget -qO- https://download.libguestfs.org/1.52-stable/libguestfs-1.52.2.tar.gz | tar xfz -
    cd libguestfs-1.52.2
    ./configure --prefix=$CEUADMIN/libguestfs/1.48.6 \
                --with-extra="findlib=$CEUADMIN/findlib/1.9.6" \
                --with-extra="hivex=$CEUADMIN/hivex/1.3.23"
    

    It appears export LIBGUESTFS_BACKEND=direct is working. 

  69. MS-GF+

    A test.sh using examples from the source (msgfplus-2024.03.26.tar.gz – assuming it has bene untarred into src/),

    ln -s src/src/test/resources test
    java -Xmx4000M -jar MSGFPlus.jar -s test/test.mgf -o test/test.mzid \
         -d test/BSA.fasta -t 10ppm -m 0 -inst 1 -e 1 -ti -1,2 -ntt 1 -tda 1 -minLength 6 \
         -maxLength 50 -n 1 -thread 7 -mod test/Mods.txt
    java -Xmx4000M -jar MSGFPlus.jar -s test/test.mgf -o test/test.mzid \
         -d  test/BSA.fasta -conf test/MSGFDB_Param.txt
    

  70. FragPipe

    It does require Java 11, MSFragger 4.1, Python 3.9, and EasyPQp; to get around we use openjdk/11.0.12_7/gcc/czpuqhmv, ceuadmin/MSFragger/4.1, ceuadmin/Anaconda3/2023.09-0.

    source /usr/local/Cluster-Apps/ceuadmin/Anaconda3/2023.09-0/bin/activate
    pip install git+https://github.com/grosenberger/easypqp.git@master
    

    IonQuant 1.10.27 is installed similarly. In fact, it is is straightforwad to select Download Update from the menu, so IonQuant-1.10.27.jar, /MSFragger-4.1/, and diaTracer-1.1.5.jar are available from the tools/ directory. 

  71. jasper

    wget -qO- https://github.com/jasper-software/jasper/archive/version-4.2.4/jasper-4.2.4.tar.gz | \
    tar -xvzf -
    module load texlive
    cd jasper-version-4.2.4/build && ./build_all
    ll ../tmp_cmake/release-1 -rt
    

  72. curl

    wget -qO- wget https://curl.se/download/curl-7.85.0.tar.gz | \
    tar xfz -
    cd curl-7.85.0/
    module load ceuadmin/openssl/3.2.1
    configure --prefix=$CEUADMIN/curl/7.85.0 --with-openssl
    make
    make install
    

  73. libjpeg-turbo

    wget -qO- https://github.com/libjpeg-turbo/libjpeg-turbo/archive/refs/tags/3.0.4.tar.gz | \
    tar xvfz -
    cd libjpeg-turbo-3.0.4/
    mkdir build
    cd build
    cmake -G"Unix Makefiles" -DCMAKE_INSTALL_PREFIX=$CEUADMIN/libjpeg-turbo/3.0.4 ..
    make
    make install
    

  74. libgeotiff

    module load ceuadmin/autoconf/2.72c.24-8e728
    module load ceuadmin/proj/7.2.1
    module load ceuadmin/libjpeg-turbo/3.0.4
    module load zlib/1.2.11
    wget -qO- https://github.com/OSGeo/libgeotiff/archive/refs/tags/1.7.3.tar.gz | \
    tar xvfz -
    cd libgeotiff-1.7.3/
    cd libgeotiff
    autoupdate
    autogen.sh
    configure --prefix=$CEUADMIN/libgeotiff/1.7.3 \
              --with-jpeg=$CEUADMIN/libjpeg-turbo/3.0.4 \
              --with-libtiff=$CEUADMIN/tiff/4.6.0 \
              --with-proj=$CEUADMIN/proj/7.2.1 \
              --with-zlib=/usr/local/Cluster-Apps/zlib/1.2.11
    make -j3
    make check
    make install
    

  75. gdal 3.7.0

    Web: https://gdal.org/en/latest/development/building_from_source.html

    wget -qO- https://github.com/OSGeo/gdal/releases/download/v3.7.0/gdal-3.7.0.tar.gz | \
    tar xvfz -
    cd gdal-3.7.0
    mkdir build && cd build
    
    module load ceuadmin/curl/7.85.0
    module load ceuadmin/libiconv/1.17
    module load ceuadmin/libarchive/3.7.5
    module load ceuadmin/libgeotiff/1.7.3
    module load ceuadmin/libjpeg-turbo/3.0.4
    module load ceuadmin/libpng/1.5.30
    module load ceuadmin/openssl/3.2.1
    module load ceuadmin/poppler/0.84.0
    module load ceuadmin/tiff/4.6.0
    
    cmake -DGDAL_ENABLE_CURL=ON \
          -DGDAL_ENABLE_OGR=ON \
          -DGDAL_ENABLE_LIBARCHIVE=ON \
          -DGDAL_ENABLE_OPENSSL=ON \
          -DCMAKE_INSTALL_PREFIX=$CEUADMIN/gdal/3.7.0 \
          -DCURL_INCLUDE_DIR=$CEUADMIN/curl/7.85.0/include \
          -DCURL_LIBRARY_RELEASE=$CEUADMIN/curl/7.85.0/lib/libcurl.so \
          -DGEOTIFF_INCLUDE_DIR=$CEUADMIN/libgeotiff/1.7.3/include \
          -DGEOTIFF_LIBRARY_RELEASE=$CEUADMIN/libgeotiff/1.7.3/lib/libgeotiff.so \
          -DARCHIVE_INCLUDE_DIR=$CEUADMIN/libarchive/3.7.5/include \
          -DARCHIVE_LIBRARY=$CEUADMIN/libarchive/3.7.5/lib/libarchive.so \
          -DCRYPTOPP_INCLUDE_DIR=$CEUADMIN/cryptopp/8.9.0/include \
          -DCRYPTOPP_LIBRARY_RELEASE=$CEUADMIN/cryptopp/8.9.0/lib/libcryptopp.so \
          -DIconv_INCLUDE_DIR=$CEUADMIN/libiconv/1.17/include \
          -DIconv_LIBRARY=$CEUADMIN/libiconv/1.17/lib/libiconv.so \
          -DJPEG_INCLUDE_DIR=$CEUADMIN/libjpeg-turbo/3.0.4/include \
          -DJPEG_LIBRARY_RELEASE=$CEUADMIN/libjpeg-turbo/3.0.4/lib64/libjpeg.so \
          -DOPENSSL_INCLUDE_DIR=$CEUADMIN/openssl/3.2.1/include \
          -DOPENSSL_CRYPTO_LIBRARY=$CEUADMIN/openssl/3.2.1/lib/libcrypto.so \
          -DOPENSSL_SSL_LIBRARY=$CEUADMIN/openssl/3.2.1/lib/libssl.so \
          -DPNG_PNG_INCLUDE_DIR=$CEUADMIN/libpng/1.5.30/include \
          -DPNG_LIBRARY_RELEAS=$CEUADMIN/libpng/1.5.30/lib \
          -DPoppler_INCLUDE_DIR=$CEUADMIN//poppler/0.84.0/include \
          -DPoppler_LIBRARY=$CEUADMIN/poppler/0.84.0/lib64/libpoppler.so \
          -DPROJ_LIBRARY=$CEUADMIN/proj/7.2.1/lib/libproj.so \
          -DPROJ_INCLUDE_DIR=$CEUADMIN/proj/7.2.1/include \
          -DTIFF_LIBRARY=$CEUADMIN/tiff/4.6.0/lib/libtiff.so \
          -DTIFF_INCLUDE_DIR=$CEUADMIN/tiff/4.6.0/include \
          ..
    make
    module load ceuadmin/Anaconda3/2023.09-0
    pip install rasterio
    pip install geopandas
    pip install gdal==3.7.0
    

    where pip install gdal uses libgdal.so just built. 

  76. inetutils

    This is already in the list of decommissioned GNU packages, https://www.gnu.org/software/software.en.html; nevertheless finger is still useful from Fedora 28. 

  77. node

    See https://cambridge-ceu.github.io/csd3/applications/node.html

  78. chrome

    wget https://dl.google.com/linux/direct/google-chrome-stable_current_x86_64.rpm
    rpm2cpio google-chrome-stable_current_x86_64.rpm | cpio -idmv
    

  79. brotli

    There appears to be CMake-based, an overhaul of 1.0.9 as used for building RStudio earlier.

    wget -qO- https://github.com/google/brotli/archive/refs/tags/v1.1.0.tar.gz | \
    tar xfz -
    cd brotli-1.1.0
    mkdir build && cd build
    cmake -DCMAKE_INSTALL_PREFIX=${CEUADMIN}/brotli/1.1.0 ..
    make
    make install
    

    As it is used for building R 4.4.2-gcc11, it also does away with gcc/6 and miniconda3/4.5.1. 

  80. Rust

    This is upgraded from 1.74.1 with rustup default stable at suggestion of gmake when compiling firefox/nightly. To avoid duplication, a symbolic link is generated on /usr/local/Cluster-Apps/ceuadmin/rust/1.74.1/cargo as ${HOME}/.cargo. Naturally, both cargo and rustc use the directory above.

    The following steps are sketched for ceuadmin/nightly,

    export CARGO_HOME="$CEUADMIN/rust/nightly/cargo"
    export RUSTUP_HOME="$CEUADMIN/rust/nightly/rustup"
    curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
    export PATH="$CARGO_HOME/bin:$PATH"
    rustup toolchain install nightly
    rustup component add rust-src --toolchain nightly-x86_64-unknown-linux-gnu
    rustup default nightly
    rustc --version
    

    As noted in rust.md on 22/5/2025, we have rustc 1.89.0-nightly (bf64d66bd 2025-05-21) 2

  81. git/2.48.1

    Now it has a separate entry in the Applications section, https://cambridge-ceu.github.io/csd3/applications/git.html

  82. libgcrypto

    wget -qO- https://gnupg.org/ftp/gcrypt/libgcrypt/libgcrypt-1.5.3.tar.bz2 | x
    tar xjf -
    mv libgcrypt-1.5.3/ src
    cd src
    ./configure --prefix=$CEUADMIN/libgcrypt/1.5.3
    make
    make install
    

  83. texinfo

    wget -qO- https://ftp.gnu.org/gnu/texinfo/texinfo-7.2.tar.xz | \
    tar Jxf -
    mv texinfo-7.2/ src
    cd src
    make && make install
    

  84. ollama

    It is rather standard,

    curl -L https://ollama.com/download/ollama-linux-amd64.tgz | \
    tar xvfz -
    ollama --help
    ollama serve &
    ollama list
    

    Note that ollama serve command procedes ollama list for available models, and the --help option will list environment variables such as OLLAMA_HOST (default 127.0.0.1:11434). 

  85. tesseract

    See https://cambridge-ceu.github.io/csd3/applications/tesseract.html

  86. apidog

    wget https://file-assets.apidog.com/download/Apidog-linux-latest.zip
    unzip  Apidog-linux-latest.zip
    ./Apidog.AppImage  --appimage-extract
    ./apidog --no-sandbox --help
    

  87. Anaconda3

    We start with

    https://repo.anaconda.com/archive/Anaconda3-2024.10-1-Linux-x86_64.sh
    PREFIX=/usr/local/Cluster-Apps/ceuadmin/Anaconda3/2024.10-1
    conda config --set auto_activate_base false
    

    Due to its complex environment, it is prohibitive to furnish any installation therefore preferable to create new environment from this.

    source /rds/project/rds-4o5vpvAowP0/software/Anaconda3-2024.10-1/bin/activate
    conda create --name new_env python=3.9
    conda activate new_env
    conda config --add channels defaults
    conda config --add channels bioconda
    conda config --add channels conda-forge
    conda install -c openms pyopenms --yes
    

  88. micromamba

    Web: https://mamba.readthedocs.io/en/latest/index.html

    export dst=/rds/project/rds-4o5vpvAowP0/software/micromamba/2.0.7
    mkdir -p $dst && cd $dst
    curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | \
    tar -xvj bin/micromamba
    export MAMBA_ROOT_PREFIX=$dst
    eval "$(./bin/micromamba shell hook -s posix)"
    micromamba activate
    micromamba install python=3.13 jupyter -c conda-forge
    export MAMBA_ROOT_PREFIX=$CEUADMIN/micromamba/2.0.7
    mkdir $CEUADMIN/micromamba
    ln -sf $dst $CEUADMIN/micromamba/2.0.7
    # current shell
    eval "$(micromamba shell hook --shell bash)"
    micromamba activate
    micromamba deactivate
    

    Note that to save space, a symbolic link is created from the project space. The usual environment creation also works,

    micromamba create -n micromamba xtensor -c conda-forge
    micromamba activate micromamba
    micromamba config append channels conda-forge
    micromamba config set channel_priority strict
    

  89. DIA-NN 2.0.2

    GitHub, https://github.com/vdemichev/DiaNN

    We see

    ./diann
    ./diann: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by ./diann)
    ./diann: /lib64/libc.so.6: version `GLIBC_2.32' not found (required by ./diann)
    ./diann: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by ./diann)
    ./diann: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by ./diann)
    

    and resort to singularity with diann-2.0.2.def

    singularity build diann.sif diann.def
    singularity run diann.sif --fasta /path/to/human_proteome.fasta --dir /path/to/data/ --out output.txt
    

  90. firefox/60.5.1-1.el7

    This is actually the only version (from shub://nuitrcs/singularity-firefox) which works on CSD3. 

  91. llama.cpp

    See https://cambridge-ceu.github.io/csd3/applications/llama.cpp.html 2

  92. InstaNovo

    See https://cambridge-ceu.github.io/csd3/Python/InstaNovo.html

  93. scGPT

    See https://cambridge-ceu.github.io/csd3/Python/scGPT.html

  94. scanpy

    GitHub: https://github.com/scverse/scanpy

    This is a side-product of scGPT (the GitHub installation above). We intend to run tutorials tutorial_pearson_residuals.ipynb as in https://github.com/scverse/scanpy-tutorials but gets error, so we set for an update of 1.11.1.

    pip uninstall scanpy -y
    pip install scanpy
    pip list | grep scanpy
    

    It turns out it does not introduce any conflicts. For this tutorial we additionally have tqdm 4.67.1 and iprogress 1.17.0. 

  95. DrugAssist

    See https://cambridge-ceu.github.io/csd3/Python/DrugAssist.html

  96. uv

    Web, https://docs.astral.sh/uv/

    curl -LsSf https://astral.sh/uv/install.sh | sh
    

    extracts uv/uvx to $HOME/.local/bin and adds . "$HOME/.local/bin/env" to $HOME/.bashrc but we might as well customise. 

  97. BitNet

    See https://cambridge-ceu.github.io/csd3/Python/BitNet.html

  98. C2S-Scale

    See https://cambridge-ceu.github.io/csd3/Python/C2S-Scale.html

  99. mozbuild

    The cluster includes cbindgen/0.28.0, clang/19.1.7, dump_syms/2.3.4, nasm/2.16.03, node/18.19.0 and pkg-config/1.8.0 from compiling mozilla Firefox nightly. By default, the directory is $HOME/.mozbuild which could also be symbolic to a designated directory. 

  100. GENIE

    git clone https://github.com/sriramlab/GENIE.git
    cd GENIE
    git checkout v1.1.1
    mkdir 1.1.1 && cd 1.1.1
    cmake ..
    make
    

  101. PGS-CSx

    Web: https://github.com/getian107/PRScsx

    The Python packages numpy and scipy are required, which are conveniently derived from ceuadmin/scGPT, and the documenetation example is used as follows,

    #!/usr/bin/bash
    module load ceuadmin/PGS-CSx
    python ${PGS_CSx_ROOT}/PRScsx.py
           --ref_dir=${LD_UKBB} \
           --bim_prefix=test_data/test \
           --sst_file=test_data/EUR_sumstats.txt,test_data/EAS_sumstats.txt \
           --n_gwas=200000,100000 \
           --pop=EUR,EAS \
           --chrom=22 \
           --phi=1e-2 \
           --out_dir=. \
           --out_name=test
    

    to get test_EAS_pst_eff_a1_b0.5_phi1e-02_chr22.txt and test_EUR_pst_eff_a1_b0.5_phi1e-02_chr22.txt.

    From snpinfo_mult_ukbb_hm3 it is apparent that the software uses GRCh37/hg19 alignment. 

  102. RSEM

    One can directly use Makefile,

    make install prefix=/usr/local/Cluster-Apps/ceuadmin/RSEM/1.3.3
    make clean
    

    The R/EBSeq package is provided but the latest version can be installed with BiocManager::install("EBSeq") from R. The pRSEM/ directory is somewhat outdated. 

  103. VirtualBox/7.1-7.1.8_168469

    This is purely experimental and half-way done. 

  104. vdo

    There is no immediate use of this but a patch to LVM2/2.03.23-icelake mysteriously built earlier.

    wget -qO- https://github.com/dm-vdo/vdo/archive/refs/tags/8.3.1.1.tar.gz | \
    tar xfz -
    cd vdo-8.3.1.1/
    make
    make install DESTDIR=$CEUADMIN/vdo/8.3.1.1 INSTALLOWNER= defaultdocdir= defaultlicensedir=
    # LVM2 as above but also into vdo/8.3.1.1
    module load ceuadmin/vdo
    cd LVM2.2.03.23
    ./configure --prefix=$CEUADMIN/LVM2/2.03.23-icelake
    make
    make install
    

  105. edit

    This is done as documented after ceuadmin/rust/nightly80 is set up,

    wget -qO- https://github.com/microsoft/edit/archive/refs/tags/v1.0.0.tar.gz | \
    tar xfz -
    cd edit-1.0.0/
    RUST_BACKTRACE=1
    cargo build --config .cargo/release.toml --release
    

    We have target/release/edit, which is from $CEUADMIN/rust/nightly/cargo/bin/cargo not from $CEUADMIN/rust/nightly/rustup/toolchains/stable-x86_64-unknown-linux-gnu/bin/cargo

  106. SQLite

    It is standard, but TCLLIBDIR is needed to relocate libtclsqlite3.so.

    wget https://www.sqlite.org/2025/sqlite-src-3490200.zip
    unzip sqlite-src-3490200.zip
    cd sqlite-src-3490200
    ./configure --enable-all --prefix=$CEUADMIN/sqlite/3.49.2  TCLLIBDIR=$CEUADMIN/sqlite/3.49.2/tcl8.6
    make && make install
    

  107. Zettlr

    Relevant information on Zettlr and Better BibTex for Zotero plugin (https://retorque.re/zotero-better-bibtex/index.html) is as follows,

    wget https://github.com/Zettlr/Zettlr/releases/download/v3.5.1/Zettlr-3.5.1-x86_64.rpm
    rpm2cpio Zettlr-3.5.1-x86_64.rpm | cpio -idmv
    wget https://github.com/retorquere/zotero-better-bibtex/releases/download/v6.7.269/zotero6-better-bibtex-6.7.269.xpi
    

    Note that a Zotero 6 Plugin is used. See https://docs.zettlr.com/en/core/citations/ for additional information. 

  108. edlib

    wget -qO- https://github.com/Martinsos/edlib/archive/refs/tags/v1.2.7.tar.gz | tar tvfz -
    cd edlib-1.2.7/
    source ~/rds/software/py38/bin/activate
    make
    

  109. SVanalyzer

    Web: https://svanalyzer.readthedocs.io/

    module load ceuadmin/Miniconda3/22.9.0
    mkdir SVanalyzer
    cd SVanalyzer/
    conda create -n 0.36
    conda activate 0.36
    conda install -c bioconda svanalyzer
    svanalyzer benchmark
    

    The bundle includes bedtools/2.30.0, edlib/1.2.3, mummer/3.23, samtools/1.3.1. An attempt from source turned to be difficult with Log-Log4perl/1.57 and/or associates though the module does proceed,

    tar xvfz /home/jhz22/.cpan/sources/authors/id/E/ET/ETJ/Log-Log4perl-1.57.tar.gz
    cd Log-Log4perl-1.57/
    export PERL5LIB=/usr/local/Cluster-Apps/ceuadmin/lib/perl5
    make install
    perl Makefile.PL INSTALL_BASE=$PERL5LIB
    make
    make install
    

    By-products include newer modules bedtools/2.29.2, edlib/1.2.7, MUMmer/4.0.1, samtools/1.20. 

  110. sniffles

    see https://cambridge-ceu.github.io/csd3/Python/Sniffles.html

  111. awscli

    See https://cambridge-ceu.github.io/csd3/applications/awscli.html

  112. SEQPower

    See https://cambridge-ceu.github.io/csd3/applications/SEQPower.html

  113. truvari

    This is analogous to sniffles but from conda install Truvari.

    wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz
    wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz.tbi
    wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.bed
    truvari bench --base HG002_SVs_Tier1_v0.6.vcf.gz \
                  --comp HG002_PacBio-HiFi-Revio_20231031_48x_GRCh38-GIABv3.vcf.gz \
                  --reference GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta.gz \
                  --includebed HG002_SVs_Tier1_v0.6.bed \
                  --output truvari_HG002_bench \
                  --giabreport --passonly --multimatch --refdist 2000 --chunksize 2000 --pctsize 0.70 --pctovl 0.0
    

    the output is in truvari_HG002_bench/. 

  114. hap.py

    See https://cambridge-ceu.github.io/csd3/Python/hap.py.html

  115. rtg-tools

    It is very straightforward,

    wget https://github.com/RealTimeGenomics/rtg-tools/releases/download/3.13/rtg-tools-3.13-linux-x64.zip
    unzip rtg-tools-3.13-linux-x64.zip
    cd benchmarking
    FA=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
    SDF=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.sdf
    rtg format -o "$SDF" "$FA"
    

    which contains part of happy.sb114 from above. 

  116. fly

    Web: https://fly.io/

    The module is built around attempt for a user,

    cd ~/rsd/software
    mkdir fly && cd fly
    ln -s /rds/project/rds-4o5vpvAowP0/software/fly ~/.fly
    curl -L https://fly.io/install.sh | sh
    export FLYCTL_INSTALL=~/.fly
    export PATH="$FLYCTL_INSTALL/bin:$PATH"
    flyctl --help
    flyctl version
    fly volumes create coffeeshop_vol --size 1
    fly deploy
    

    The last two lines are per https://github.com/pavelanni/pythonicadventure-code

  117. cli (GitHub CLI)

    See https://cambridge-ceu.github.io/csd3/applications/cli.html

  118. MToolBox

    Due to its size this is recreated as a separate entry, https://cambridge-ceu.github.io/csd3/applications/MToolBox.html

  119. VS Code

    It is possible from CLI

    wget -qO- https://update.code.visualstudio.com/latest/linux-x64/stable | \
    tar -xzf -
    cd VSCode-linux-x64
    ./code
    

  120. LLM

    Web: https://llm.datasette.io/en/stable/

    export UV_TOOL_DIR=$CEUADMIN/llm/0.26
    uv tool install llm
    uv tool dir
    

  121. haplogrep

    This follows MToolBox, see https://cambridge-ceu.github.io/csd3/applications/haplogrep.html

  122. flashpca

    This module is built to mirror flashpca2/2 which has been linked to personal home folder. 

  123. fNUMT

    This suite includes blastn 2.13.0+, samtools 1.10 and cap3 02/10/15. 

  124. simNGS

    Case study from

    Zhuang X, et al. Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma. Genome Med 16, 50 (2024). https://doi.org/10.1186/s13073-024-01319-2.

    cat mutated_rCRS.fa | simLibrary -x 5 -r 150 --seed 12 > chrM_mut_5x.fasta
    cat wide_rCRS.fa | simLibrary-x 4995 -r 150 --seed 12 > chrM_wide_4995x.fasta
    cat chrM_mut_5x.fasta chrM_wide_4995x.fasta > chrM_sim_5000x_mut5x.fasta
    simNGS -p "paired" -O "chrM_sim_5000x_mut5x_PE150" -o "fastq" -s 12 runfile chrM_sim_5000x_mut5x.fasta