ceuadmin

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

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

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). A large collection of R packages (1,300 as of 23/4/2023) is linked with the latest R distribution, 4.3.0.

For CEU users, it is easy to point to them, e.g.,

export HPC_WORK=/rds/user/$USER/hpc-work/
export RDS=/rds/project/jmmh2/rds-jmmh2-public_databases/software
export R_LIBS=${RDS}/R:${RDS}/R-4.3.0/library

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

The following script tests for loading of dplyr:

export RDS=/rds/project/jmmh2/rds-jmmh2-public_databases/software
export PATH=${PATH}:${RDS}/R-4.3.0/bin
export R_LIBS=${RDS}/R-4.3.0/library:${RDS}/R
Rscript -e 'suppressMessages(library(dplyr));cat("OK!\n")'

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

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

For non-CEU users, please drop an email to jhz22@medschl.cam.ac.uk for access.

Entries

The current list is as follows,

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

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

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

Usage

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

module help ceuadmin/pspp

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

module load ceuadmin/pspp
psppire

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

module unload ceuadmin/pspp

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

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.

Module creation

The following example shows how to set up a module,

#!/bin/bash

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

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

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

}

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

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

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

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

Footnotes

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

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

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

    A grep of recent add-ons in the Genetics 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
    2023-02-01 GENEHUNTER/2.1_r6 Genetics
    2023-03-14 regenie/3.2.5 Genetics
    2023-03-24 PoGo/1.0.0 Genetics
    2023-03-31 PWCoCo/2023-03-31 Genetics
    2023-04-02 regenie/3.2.5.3 Genetics
    2023-04-04 PWCoCo/1.0 Genetics
    2023-06-02 regenie/3.2.7 Genetics10
    2023-06-06 allegro/2.0f Genetics

    * CEU or approved users only. ↩

  2. GUI

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

  3. 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. ↩

  10. Building regenie 3.2.7

    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

    ↩