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,
- A file named NOTE indicates the original annotation.
- A symbolic link is generated when appropriate to simplify executable file name.
- The available source package is kept in the sources/ directory.
Word cloud diagrams
They are generated from script setup.sh,
Footnotes
-
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 in2020-05-05r
indicates a replacement of functions inlibsrc/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.
-
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
-
fcgene
Alternative site
-
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. ↩
-
qtltools
The long version number is 1.3.1-25-g6e49f85f20. ↩
-
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. ↩
-
libxslt
There is complaint about docbook as in expat, however there is no apparent option to control for this. ↩
-
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
-
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=$CEUADMIN/json-c/0.17-20230812-icelake \ --with-proj=/usr/local/Cluster-Apps/ceuadmin/proj/6.3.0 \ --without-sqlite3 make
-
expat
Due to error messages, the options are specified as follows,
./configure --prefix=$CEUADMIN/expat/2.4.7 --without-docbook
-
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=$CEUADMIN/ruby/2.7.5 make make install rvm reset
-
libgit2
It uses Python 2.7 and libssh2 (as above). The following warnings are given
/usr/bin/ld: warning: libssl.so.10, needed by /home/jhz22/hpc-work/lib/libssh2.so, may conflict with libssl.so.1.1 /usr/bin/ld: warning: libcrypto.so.10, needed by /home/jhz22/hpc-work/lib/libssh2.so, may conflict with libcrypto.so.1.1
-
nettle
This is required by gnutls/3.7.8, which requires
ceuadmin/gmp/6.2.1
and--enable-mini-gmp
.Alternatively, we use
./configure --prefix=$HPC_WORK LDFLAGS=-L$HPC_WORK/lib64 LIBS=-lhogweed --disable-openssl \ --with-lib-path=/usr/local/Cluster-Apps/ceuadmin/gmp/6.2.1/lib \ --with-include-path=/usr/local/Cluster-Apps/ceuadmin/gmp/6.2.1/include
-
gnutls
It requires libunistring (optionally –with-included-unistring), libidn2, libunbound, and trousers, all prepared above.
./configure --prefix=$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 makeck_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=$CEUADMIN/gnutls/3.8.4-icelake --with-included-unistring make make install
-
lemma
The documentation indicates a requirement of gcc/9.4, boost/1.78, OpenMP/3.1 and/or Intel MKL Library 2019 Update 1 but it is possible to proceed with gcc/11, cmake-3.19.7-gcc-5.4-5gbsejo, boost-1.66.0-gcc-5.4.0-slpq3un, ceuadmin/bgen. ↩
-
The following scripts avoid option
--without-ssl
.wget -qO- https://github.com/axel-download-accelerator/axel/releases/download/v2.17.11/axel-2.17.11.tar.gz | \ tar xvfz - cd axel-2.17.11 ./configure --prefix=$CEUADMIN/axel/2.17.11 LDFLAGS=-L/usr/lib64 LIBS=-lssl
-
OpenMS
When the OpenMS module is loaded, pyopenms and alphapept also become available. ↩
-
locuszoom
The version adds chromosome X data and will have options using INTERVAL data. ↩
-
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. ↩
-
pwcoco
It compiles under gcc/9. Upon release of 1.1, this snapshot is removed. ↩
-
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
-
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
-
quarto
See https://cambridge-ceu.github.io/csd3/applications/quarto.html. ↩
-
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
-
pspp
See https://cambridge-ceu.github.io/csd3/applications/pspp.html.
Makeinfo
The following replacement is used.
MAKEINFO = ${SHELL} '/rds/project/jmmh2/rds-jmmh2-public_databases/software/pspp-2.0.0-pre1ge32bec/build-aux/missing' makeinfo --force --no-validate
while the rest is copied from GNU build, https://benpfaff.org/~blp/pspp-master/20230624103130/x86_64/pspp-2.0.0-pre1ge32bec-x86_64-build20230624103419.tar.gz. ↩
-
ncbi-vdb
The installation is preceeded with
module load gcc/6 flex-2.6.4-gcc-5.4.0-2u2fgon
. Althoughconfigure
is provided,cmake
is used instead.cmake -DCMAKE_PREFIX_PATH=$CEUADMIN/ncbi-vdb/3.0.8 -DCMAKE_INSTALL_PREFIX=$CEUADMIN/ncbi-vdb/3.0.8 ..
-
sra-tools
First, create a symbolic link for
ncbi-vdb/3.0.8
in the parent directory.cmake -DVDB_LIBDIR=$CEUADMIN/ncbi-vdb/3.0.8/lib64 -DCMAKE_INSTALL_PREFIX=$CEUADMIN/sra-tools/3.0.8 ..
Drop
constexpr
as inconstexpr 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
. ↩ -
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 ↩
-
gdc
It also includes gdc_dtt-ui 1.0.0 ↩
-
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. ↩ -
regtools
gcc/6 is required for C++11. ↩
-
varscan
Simply call
java -jar $VARSCAN_HOME/VarScan.v2.4.6.jar
aftermodule load ceuadmin/VarScan/2.4.6
. ↩ -
tatami
The following aspects are required.
- module load gcc/9
- mkdir build && cd build
- cmake .. -DCMAKE_INSTALL_PREFIX=$CEUADMIN/tatami/2.1.2
- cmake –build . –target install
-
nextflow
curl -fsSL get.nextflow.io | bash
-
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=$CEUADMIN/singularity/4.0.3 --without-seccomp --without-conmon --without-suid cd builddir & make
-
fraposa
Several packages, including poetry, poetry-plugin-export and fraposa_pgsc, will be installed as follows,
module load ceuadmin/Anaconda3/2023.09-0 pip install poetry pip3 install poetry-plugin-export pip install --use-feature=fast-deps . scripts/run_example.sh
This is necessay since by default
peotry install
will use user's home directory. As indicated frompoetry install --help
:The install command reads the poetry.lock file from the current directory, processes it, and downloads and installs all the libraries and dependencies outlined in that file. If the file does not exist it will look for pyproject.toml and do the same. ↩
-
pgsc_calc
Application, https://pgsc-calc.readthedocs.io/en/latest/index.html
nextflow run pgscatalog/pgsc_calc -profile test,singularity
It appears quarto is called so presumably under icelake.
For 2.0.3, we try the conda option. ↩
-
deno
Web: https://anaconda.org/conda-forge/deno/files
wget https://anaconda.org/conda-forge/deno/1.40.2/download/linux-64/deno-1.40.2-hfc7925d_0.conda -O deno.conda unzip deno.conda tar --use-compress-program=unzstd -xvf pkg-deno-1.40.2-hfc7925d_0.tar.zst
-
R
This replaces R/4.3.2. It is also R/latest. ↩
-
GitKraken
This replaces 8.1.0. ↩
-
automake
This is required by pspp 2.0.0. ↩
-
openssl
Archive, https://www.openssl.org/source/old/
wget -qO- https://www.openssl.org/source/openssl-3.2.1.tar.gz | \ tar xvfz - cd openssl-3.2.1/ export PERL5LIB= ./Configure --prefix=$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=$CEUADMIN/openssl/1.1.1b-icelake/ssl make install
Module
ceuadmin/openssl/3.2.1
actually points to/usr/local/Cluster-Apps/openssl/3.2.1
. ↩ -
openssh
OpenSSL is called first to use the specific
openssl
, e.g.,module load ceuadmin/openssl/3.2.1-icelake ./configure --prefix=$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. ↩ -
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 specifyo 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. ↩
-
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
-
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=$CEUAMIN/LVM2/2.03.23-icelake --with-vdo=none make device-mapper make install_device-mapper
-
cryptosetup
# incomplete libssh in need of a fix module load cmake/3.21.3/intel/wce32356 wget -qO- https://www.libssh.org/files/0.10/libssh-0.10.6.tar.xz | \ tar xfJ - cd libssh-0.10.6 mkdir build && cd build cmake -DCMAKE_INSTALL_PREFIX=$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=$CEUADMIN/cryptsetup/2.7.1-icelake --disable-ssh-token
-
krb5-icelake
It is possible to use the default ssh.
configure --prefix=$CEUADMIN/krb5/1.21.2-icelake module load gettext/0.21/gcc/qnrcglqo make install
-
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=${CEUADMIN}/git/2.44.0-icelake make make install
There remains an error message
git-remote-https: symbol lookup error: /usr/lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b
. ↩ -
peer
This is documented separately in the R section, https://cambridge-ceu.github.io/csd3/applications/peer.html. ↩
-
ImageMagick
wget -qO- https://github.com/ImageMagick/ImageMagick/archive/refs/tags/7.1.1-31.tar.gz | \ tar xvfz - cd ImageMagick-7.1.1-31/ ./configure --prefix=$CEUADMIN/ImageMagick/7.1.1-31 make make install
-
rtmpdump
It is necessary for
RCurl 1.98-1.14
. Withcurl-7.63.0-gcc-5.4.0-4uswlql
we could also installrtracklayer 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")'
-
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
-
crux
See https://cambridge-ceu.github.io/csd3/applications/crux.html. ↩
-
p7zip-zstd
A simple
make
is sufficient but it is necessary to implement a minor revision ofinstall.sh
, line 19, so thatDEST_HOME=/usr/local/Cluster-Apps/ceuadmin/p7zip-zstd/17.05
. ↩ -
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=$CEUADMIN/boost/1.76.0 install ./bjam --with-regex --with-filesystem --with-iostreams --with-thread --with-program_options \ --with-serialization --with-system --with-date_time install export BOOST_ROOT=/usr/local/src/boost_1_76_0
-
wine
module load ceuadmin/krb5/1.21.2-icelake configure --prefix=${CEUADMIN}/wine/8.21 --enable-win64 make install
-
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}
-
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 ```
-
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
${FLASHLFQ_ROOT}/src/Test/SampleFiles
.module load ceuadmin/FlashLFQ flashlfq --idt MaxQuant/msms.txt --rep . --ppm 5 --chg
which works on
MaxQuant/msms.txt
and generatesFlashLfqSettings.toml
,QuantifiedPeaks.tsv
,QuantifiedPeptides.tsv
andQuantifiedProteins.tsv
. ↩ -
docker
See https://cambridge-ceu.github.io/csd3/applications/docker.html. ↩
-
podman
See https://cambridge-ceu.github.io/csd3/applications/podman.html. ↩
-
alpine
Module
ceuadmin/alpine/2.26-icelake
compiled usinggcc/11.2.0/gcc/rjvgspag
. ↩ -
qemu
See https://cambridge-ceu.github.io/csd3/applications/qemu.html. ↩
-
hivex
wget -qO- https://download.libguestfs.org/hivex/hivex-1.3.23.tar.gz | tar xfz - cd hivex-1.3.23 module load ceuadmin/ocaml/4.14.2 module load ceuadmin/ruby/2.7.5 export PERLB5LIB= autoreconf -i --force ./generator/generator.ml ./configure --prefix=$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 fromgenerator/generator.ml
.. TheINSTALL_PREFIX
is replaced withINSTALL_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
-
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
-
opam
opam init opam switch list opam switch list-available opam switch create ocaml-4.14 opam install -y hivex --destdir $CEUADMIN/hivex/1.3.23
-
libguestfs
wget -qO- https://download.libguestfs.org/1.52-stable/libguestfs-1.52.2.tar.gz | tar xfz - cd libguestfs-1.52.2 ./configure --prefix=$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. ↩ -
MS-GF+
A
test.sh
using examples from the source (msgfplus-2024.03.26.tar.gz
– assuming it has bene untarred intosrc/
),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
-
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, soIonQuant-1.10.27.jar
,/MSFragger-4.1/
, anddiaTracer-1.1.5.jar
are available from thetools/
directory. ↩ -
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
-
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=$CEUADMIN/curl/7.85.0 --with-openssl make make install
-
libjpeg-turbo
wget -qO- https://github.com/libjpeg-turbo/libjpeg-turbo/archive/refs/tags/3.0.4.tar.gz | \ tar xvfz - cd libjpeg-turbo-3.0.4/ mkdir build cd build cmake -G"Unix Makefiles" -DCMAKE_INSTALL_PREFIX=$CEUADMIN/libjpeg-turbo/3.0.4 .. make make install
-
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
-
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
useslibgdal.so
just built. ↩ -
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. ↩ -
node
See https://cambridge-ceu.github.io/csd3/applications/node.html. ↩
-
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
-
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=${CEUADMIN}/brotli/1.1.0 .. make make install
As it is used for building R 4.4.2-gcc11, it also does away with gcc/6 and miniconda3/4.5.1. ↩
-
Rust
This is upgraded from 1.74.1 with
rustup default stable
at suggestion of gmake when compiling firefox/nightly. To avoid duplication, a symbolic link is generated on/usr/local/Cluster-Apps/ceuadmin/rust/1.74.1/cargo
as${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 -
git/2.48.1
Now it has a separate entry in the Applications section, https://cambridge-ceu.github.io/csd3/applications/git.html. ↩
-
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
-
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
-
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 procedesollama list
for available models, and the--help
option will list environment variables such as OLLAMA_HOST (default 127.0.0.1:11434). ↩ -
tesseract
See https://cambridge-ceu.github.io/csd3/applications/tesseract.html. ↩
-
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
-
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
-
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
-
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
-
firefox/60.5.1-1.el7
This is actually the only version (from shub://nuitrcs/singularity-firefox) which works on CSD3. ↩
-
llama.cpp
See https://cambridge-ceu.github.io/csd3/applications/llama.cpp.html. ↩ ↩2
-
InstaNovo
See https://cambridge-ceu.github.io/csd3/Python/InstaNovo.html. ↩
-
scGPT
See https://cambridge-ceu.github.io/csd3/Python/scGPT.html. ↩
-
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 andiprogress
1.17.0. ↩ -
DrugAssist
See https://cambridge-ceu.github.io/csd3/Python/DrugAssist.html. ↩
-
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$HOME/.bashrc
but we might as well customise. ↩ -
BitNet
See https://cambridge-ceu.github.io/csd3/Python/BitNet.html. ↩
-
C2S-Scale
See https://cambridge-ceu.github.io/csd3/Python/C2S-Scale.html. ↩
-
mozbuild
The cluster includes
cbindgen/0.28.0
,clang/19.1.7
,dump_syms/2.3.4
,nasm/2.16.03
,node/18.19.0
andpkg-config/1.8.0
from compiling mozilla Firefox nightly. By default, the directory is$HOME/.mozbuild
which could also be symbolic to a designated directory. ↩ -
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
-
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
andtest_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. ↩ -
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. ↩ -
VirtualBox/7.1-7.1.8_168469
This is purely experimental and half-way done. ↩
-
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
-
edit
This is done as documented after
ceuadmin/rust/nightly
80 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
. ↩ -
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
-
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. ↩
-
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
-
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=$PERL5LIB make make install
By-products include newer modules bedtools/2.29.2, edlib/1.2.7, MUMmer/4.0.1, samtools/1.20. ↩
-
sniffles
see https://cambridge-ceu.github.io/csd3/Python/Sniffles.html. ↩
-
awscli
See https://cambridge-ceu.github.io/csd3/applications/awscli.html. ↩
-
SEQPower
See https://cambridge-ceu.github.io/csd3/applications/SEQPower.html. ↩
-
truvari
This is analogous to sniffles but from
conda install Truvari
.wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz.tbi wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.bed truvari bench --base HG002_SVs_Tier1_v0.6.vcf.gz \ --comp HG002_PacBio-HiFi-Revio_20231031_48x_GRCh38-GIABv3.vcf.gz \ --reference GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta.gz \ --includebed HG002_SVs_Tier1_v0.6.bed \ --output truvari_HG002_bench \ --giabreport --passonly --multimatch --refdist 2000 --chunksize 2000 --pctsize 0.70 --pctovl 0.0
the output is in truvari_HG002_bench/. ↩
-
hap.py
See https://cambridge-ceu.github.io/csd3/Python/hap.py.html. ↩
-
rtg-tools
It is very straightforward,
wget https://github.com/RealTimeGenomics/rtg-tools/releases/download/3.13/rtg-tools-3.13-linux-x64.zip unzip rtg-tools-3.13-linux-x64.zip cd benchmarking FA=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna SDF=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.sdf rtg format -o "$SDF" "$FA"
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fly
Web: https://fly.io/
The module is built around attempt for a user,
cd ~/rsd/software mkdir fly && cd fly ln -s /rds/project/rds-4o5vpvAowP0/software/fly ~/.fly curl -L https://fly.io/install.sh | sh export FLYCTL_INSTALL=~/.fly export PATH="$FLYCTL_INSTALL/bin:$PATH" flyctl --help flyctl version fly volumes create coffeeshop_vol --size 1 fly deploy
The last two lines are per https://github.com/pavelanni/pythonicadventure-code. ↩
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cli (GitHub CLI)
See https://cambridge-ceu.github.io/csd3/applications/cli.html. ↩
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MToolBox
Due to its size this is recreated as a separate entry, https://cambridge-ceu.github.io/csd3/applications/MToolBox.html. ↩
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VS Code
It is possible from CLI
wget -qO- https://update.code.visualstudio.com/latest/linux-x64/stable | \ tar -xzf - cd VSCode-linux-x64 ./code
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LLM
Web: https://llm.datasette.io/en/stable/
export UV_TOOL_DIR=$CEUADMIN/llm/0.26 uv tool install llm uv tool dir
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haplogrep
This follows MToolBox, see https://cambridge-ceu.github.io/csd3/applications/haplogrep.html. ↩
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flashpca
This module is built to mirror flashpca2/2 which has been linked to personal home folder. ↩
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fNUMT
This suite includes blastn 2.13.0+, samtools 1.10 and cap3 02/10/15. ↩
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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