ceuadmin

The CEU software repository is here, /usr/local/Cluster-Apps/ceuadmin/. The current list is as follows,

  [1] "ABCtoolbox"          "akt"                 "alpine"
  [4] "annovar"             "aria2"               "axel"
  [7] "bazel"               "bcftools"            "Beagle"
 [10] "bedops"              "bedtools2"           "bgen"
 [13] "biobank"             "blat"                "boltlmm"
 [16] "brotli"              "CaVEMaN"             "CAVIAR"
 [19] "CAVIARBF"            "ccal"                "circos"
 [22] "citeproc"            "cppunit"             "crossmap"
 [25] "Cytoscape"           "DEPICT"              "DjVuLibre"
 [28] "docbook2X"           "DosageConverter"     "Eagle"
 [31] "ensembl-vep"         "exiv2"               "exomeplus"
 [34] "expat"               "FastQTL"             "fcGENE"
 [37] "ffmpeg"              "fgwas"               "finemap"
 [40] "fossil"              "fribidi"             "GARFIELD"
 [43] "gcta"                "gdal"                "GEM"
 [46] "GEMMA"               "Genotype-Harmonizer" "gettext"
 [49] "ghc"                 "ghostscript"         "git"
 [52] "git-extras"          "GitKraken"           "gmp"
 [55] "gnutls"              "googletest"          "GraphicsMagick"
 [58] "GreenAlgorithms4HPC" "gtksourceview"       "gtool"
 [61] "hpg"                 "htslib"              "icu"
 [64] "impute"              "JAGS"                "jq"
 [67] "KentUtils"           "KING"                "lapack"
 [70] "ldc2"                "LDstore"             "LEMMA"
 [73] "libcares"            "libgit2"             "libglvnd"
 [76] "libiconv"            "libidn2"             "libntlm"
 [79] "libpng"              "libsodium"           "libssh2"
 [82] "libuv"               "libxml2"             "libxslt"
 [85] "locuszoom"           "MAGENTA"             "magma"
 [88] "MAGMA"               "Mega2"               "metal"
 [91] "MONSTER"             "MORGAN"              "MR-MEGA"
 [94] "MsCAVIAR"            "nano"                "ncurses"
 [97] "netbeans"            "nettle"              "NLopt"
[100] "node"                "nspr"                "oniguruma"
[103] "OpenMS"              "openssl"             "osca"
[106] "PAINTOR"             "pandoc"              "pandoc-citeproc"
[109] "parallel"            "Pascal"              "pcre2"
[112] "pdf2djvu"            "phenoscanner"        "plink"
[115] "plink-bgi"           "plinkseq"            "polyphen"
[118] "poppler"             "proj"                "PRSice"
[121] "pspp"                "qctool"              "qpdf"
[124] "qt"                  "qtcreator"           "QTLtools"
[127] "quicktest"           "R"                   "raremetal"
[130] "rclone"              "readline"            "regenie"
[133] "rstudio"             "ruby"                "samtools"
[136] "shapeit"             "SMR"                 "snakemake"
[139] "SNP2HLA"             "snptest"             "sqlite"
[142] "ssw"                 "STAR"                "stata"
[145] "SurvivalAnalysis"    "SurvivalKit"         "tabix"
[148] "tidy"                "trinculo"            "trousers"
[151] "Typora"              "unbound"             "vala"
[154] "vcftools"            "VEGAS2"              "VSCode"
[157] "yaml-cpp"            "zstd"

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

The module files are defined at /usr/local/Cluster-Config/modulefiles/ceuadmin. Most software use gcc/6; when required it can be enabled with module load gcc/6.

Most should be available to all CSD3 users at the campus, e.g., for pspp, a brief description of a module is available with

module help ceuadmin/pspp

and the module is loaded and graphical user interface (GUI)1 started with

module load ceuadmin/pspp
psppire

for PSPP 1.6.0. Once the job is done, one can restore the previous environment with

module unload ceuadmin/pspp

A full list of module subcommands is available with module help as detailed here for 3.2.9 – CSD3 uses version 3.2.10 dated 2012-12-21. In particular, module whatis ceuadmin/ensembl-vep indicates usage regarding build37/build38 setup for the loftee plugin used in loss of function (LoF) annotation.

Ideally, software with large size / reference data will be available from /rds/project/jmmh2/software. However, CEU users will be able to use ANNOVAR, ensembl-vep, OpenMS, polyphen, KentUtils/MAGMA/Pascal/VEGASV2/fgwas/locuszoom linking internal projects/personal space (additional requests need to be made). Further information is avaiiable from doc/ceuadmin.md, ceuadmin.html. A large collection of R packages (1,258 as of November 2022) is linked with ceuadmin/R/4.2.2, the latest R distribution, please drop an email to jhz22@medschl.cam.ac.uk for access. The original list prior to mid-November 2022 is given below2.

  1. GUI

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

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

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

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

    Date Add.ons Category
    2022-10-22 snptest/2.5.6 Genetics
    "" qctool/2.0.8 Genetics
    "" gcta/1.94.1 Genetics
    "" KING/2.1.6 Genetics
    "" LDstore/2.0 Genetics
    "" shapeit/3 Genetics
    "" vcftools/0.1.16 Genetics
    "" finemap/1.4 Genetics
    2022-10-23 quicktest/1.1 Genetics
    "" samtools/1.11 Genetics
    "" bcftools/1.12 Genetics
    "" MORGAN/3.4 Genetics
    "" METAL/2020-05-05r Genetics3
    "" regenie/3.2.1 Genetics
    "" GEMMA/0.98.5 Genetics4
    "" htslib/1.12 Genetics
    "" fcGENE/1.0.7 Genetics5
    "" SMR/1.0.3 Genetics
    "" FastQTL/2.165 Genetics
    2022-10-26 circos/0.69-9 Genetics
    "" bgen/1.1.7 Genetics
    "" DosageConverter/1.0.0 Genetics
    "" QTLtools/1.3.1-25 Genetics6
    "" blat/37x1 Genetics
    "" bedtools2/2.29.2 Genetics
    "" bedops/2.4.41 Genetics
    2022-11-03 Beagle/3.0.4 Genetics
    2022-11-08 CrossMap/0.6.4 Genetics
    "" SurvivalKit/6.12 Genetics
    "" PRSice/2.3.3 Genetics
    2022-11-09 qctool/2.2.0 Genetics
    2022-11-10 CaVEMaN/1.01-c1815a0 Genetics
    "" akt/0.3.3 Genetics
    "" MsCAVIAR/0.6.4 Genetics
    "" CAVIAR/2.2 Genetics
    "" MONSTER/1.3 Genetics
    "" osca/0.46 Genetics
    "" LEMMA/1.0.4 Genetics7
    "" CAVIARBF/0.2.1 Genetics
    2022-11-11 PAINTOR/3.0 Genetics
    2022-11-14 MR-MEGA/0.2 Genetics
    2022-11-16 SNP2HLA/1.0.3 Genetics
    "" STAR/2.7.10b Genetics
    "" Mega2/6.0.0 Genetics
    2022-11-19 ensembl-vep/104 Genetics*
    "" OpenMS/3.0.0 Genetics*8
    "" 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*9
    "" DEPICT/v1_rel194 Genetics*
    "" MAGMA/1.10 Genetics*
    "" Pascal/v_debut Genetics*
    "" VEGAS2/2.01.17 Genetics*
    "" fgwas/0.3.6 Genetics*
    2022-12-04 phenoscanner/v2 Genetics*
    2022-12-07 SurvivalAnalysis/2016-05-09 Genetics
    2023-01-03 Eagle/2.4.1 Genetics
    2023-01-05 GEM/1.4.5 Genetics

    * CEU or approved users only. ↩

  3. 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.

    ↩

  4. 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

    ↩

  5. Alternative site

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

  6. The long version number is 1.3.1-25-g6e49f85f20. ↩

  7. 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/1.1.7. ↩

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

  9. locuszoom

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