A full of ceuadmin modules

Location at CSD3: /usr/local/Cluster-Apps/ceuadmin, (module files: /usr/local/Cluster-Config/modulefiles/ceuadmin)

The current list is as follows1,

  [1] "ABCtoolbox"            "akt"                   "allegro"
  [4] "alpine"                "Anaconda3"             "annovar"
  [7] "aria2"                 "autoconf"              "axel"
 [10] "bazel"                 "bcftools"              "Beagle"
 [13] "bedops"                "bedtools2"             "bgen"
 [16] "biobank"               "blat"                  "boltlmm"
 [19] "brotli"                "busybox"               "CaVEMaN"
 [22] "CAVIAR"                "CAVIARBF"              "ccal"
 [25] "circos"                "citeproc"              "cppunit"
 [28] "crossmap"              "Cytoscape"             "DEPICT"
 [31] "DjVuLibre"             "docbook2X"             "DosageConverter"
 [34] "Eagle"                 "enchant"               "ensembl-vep"
 [37] "exiv2"                 "exomeplus"             "expat"
 [40] "FastQTL"               "fcGENE"                "ffmpeg"
 [43] "fgwas"                 "finemap"               "fossil"
 [46] "fribidi"               "GARFIELD"              "gatk"
 [49] "gcta"                  "gdal"                  "gdc"
 [52] "geany"                 "GEM"                   "GEMMA"
 [55] "Genotype-Harmonizer"   "gettext"               "gh"
 [58] "ghc"                   "ghostscript"           "git"
 [61] "git-extras"            "GitKraken"             "glib"
 [64] "globusconnectpersonal" "gmp"                   "gnutls"
 [67] "googletest"            "graphene"              "GraphicsMagick"
 [70] "GreenAlgorithms4HPC"   "gsl"                   "gtk+"
 [73] "gtksourceview"         "gtool"                 "hpg"
 [76] "htslib"                "hunspell"              "icu"
 [79] "ImageJ"                "impute"                "JabRef"
 [82] "JAGS"                  "jq"                    "KentUtils"
 [85] "KING"                  "lapack"                "ldc2"
 [88] "ldsc"                  "LDstore"               "LEMMA"
 [91] "libcares"              "libgit2"               "libglvnd"
 [94] "libiconv"              "libidn2"               "libntlm"
 [97] "libpng"                "libsodium"             "libssh2"
[100] "libuv"                 "libxml2"               "libxslt"
[103] "locuszoom"             "MAGENTA"               "magma"
[106] "Mega2"                 "metal"                 "MONSTER"
[109] "MORGAN"                "MR-MEGA"               "MsCAVIAR"
[112] "nano"                  "ncbi-vdb"              "ncurses"
[115] "netbeans"              "nettle"                "NLopt"
[118] "node"                  "nspr"                  "oniguruma"
[121] "openjdk"               "OpenMS"                "openssl"
[124] "osca"                  "PAINTOR"               "pandoc"
[127] "pandoc-citeproc"       "pango"                 "parallel"
[130] "Pascal"                "pcre2"                 "pdf2djvu"
[133] "pdfjam"                "phenoscanner"          "PhySO"
[136] "plink"                 "plink-bgi"             "plinkseq"
[139] "PoGo"                  "polyphen"              "poppler"
[142] "proj"                  "PRSice"                "pspp"
[145] "PWCoCo"                "qctool"                "qpdf"
[148] "qt"                    "qtcreator"             "QTLtools"
[151] "quarto"                "quicktest"             "R"
[154] "raremetal"             "rclone"                "readline"
[157] "regenie"               "RHHsoftware"           "rst2pdf"
[160] "rstudio"               "ruby"                  "samtools"
[163] "shapeit"               "SMR"                   "snakemake"
[166] "SNP2HLA"               "snptest"               "spread-sheet-widget"
[169] "sqlite"                "sra-tools"             "ssw"
[172] "STAR"                  "stata"                 "SurvivalAnalysis"
[175] "SurvivalKit"           "tabix"                 "thunderbird"
[178] "tidy"                  "trinculo"              "trousers"
[181] "Typora"                "unbound"               "vala"
[184] "vcftools"              "VEGAS2"                "VSCode"
[187] "vte"                   "xpdf"                  "yaml-cpp"
[190] "Zotero"                "zstd"

Most should be available to all CSD3 users in the whole 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)2 started with

module load ceuadmin/pspp

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 commands is available with module help.

NB most software use gcc/6, which can be enabled with module load gcc/6.

Due to limitation in size, a trade-off has been made to make some software available for CEU users by linking internal folders: ensembl-vep, ANNOVAR, polyphen, OpenMS, GARFIELD, KentUtils, (with large collection of packages), locuszoom (adding chromosome X data). Others which is in condieration include depict, fastenloc (with GTEx v8 reference data), tensorqtl, CookHLA, HLA-TAPAS, HATK. A desirable location is /rds/project/jmmh2/software.

All recent entries

They 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 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
"" GitKraken/8.1.0 Generic
2022-10-24 Typora/0.11.8beta Generic
"" pandoc/2.19.2 Generic
"" citeproc/ Generic
"" citeproc/ Generic
2022-10-26 circos/0.69-9 Genetics
"" DjVuLibre/ 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 Generic6
"" DosageConverter/1.0.0 Genetics
"" tidy/5.8.0 Generic
2022-10-29 ghc/8.6.5 Generic
"" pandoc-citeproc/ 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 Genetics7
"" 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 Generic8
"" 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 Generic9
"" libssh2/1.10.0 Generic
"" libxml2/2.9.10 Generic10
"" libsodium/1.10.0 Generic
"" gdal/3.0.4 Generic11
"" expat/2.4.7 Generic12
"" 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 Generic
2022-11-06 libpng/0.5.30 Generic
"" libgit2/1.1.0 Generic13
"" 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 Generic14
"" gnutls/3.7.8 Generic15
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 Genetics16
"" 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 Generic17
"" 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*18
"" 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*19
"" 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 Generic20
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 Genetics21
2023-04-02 regenie/ 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 Genetics22
2023-06-05 gsl/2.7.1 Generic
2023-06-06 allegre/2.0f Genetics
2023-06-14 autoconf/2.72c.24-8e728 Generic23
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
2023-08-02 fossil/2.22 Generic
2023-08-04 quarto/1.3.450-icelake Generic24
2023-08-06 finemap/1.4.2 Genetics
2023-08-10 GreenAlgorithmsforHPC/0.3 Generic
2023-08-12 xpdf/4.04 Generic25
!2023-08-22 thunderbird/115.1.1 Generic
!2023-08-24 pdfjam/3.07 Generic
2023-09-03 2.0.0-pre1ge32bec Genetic26
2023-09-03 spead-sheet-widget Generic
2023-09-27 ncbi-vdb/3.0.8 Genetics27
2023-09-27 sra-tools/3.0.8 Genetics28
2023-09-27 gatk/ Genetics29
2023-09-28 openjdk/8u382-b05 Generic
2023-09-28 openjdk/11.0.20+8 Generic
2023-09-28 openjdk/17.0.8+7 Generic
2023-10-24 rst2pdf/0.101 Generic
2023-10-24 geany/1.38 Generic
2023-10-24 pango/1.41.1 Generic
2023-10-24 gettext/0.20 Generic
2023-10-26 glib/2.58.3 Generic
2023-10-27 graphene/1.4.0 Generic
2023-10-27 graphene/1.8.0 Generic
2023-10-24 gtk+/3.24.0 Generic
2023-10-24 geany/2.0 Generic
2023-10-28 hunspell/1.7.0 Generic
2023-10-28 hunspell/1.7.2 Generic
2023-10-28 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 Genetics30

* CEU or approved users only.

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.

# 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

  1. The list is generated and the number counted with

    Rscript -e 'setdiff(dir(),c("doc","lib","misc","sources"))'
    # Generic, Genetics, All
    grep -e Generic ceuadmin.md | grep "^[|]" | wc -l
    grep -e Genetics ceuadmin.md | grep "^[|]" | wc -l
    grep -e Genetics -e Generic ceuadmin.md | grep "^[|]" | wc -l

    The latest R (4.2.2 as of 31/10/2022) is installed but a larger collection of packages will be deposited at /rds/project/jmmh2. 

  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.

    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

  5. Alternative site

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

  6. 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. 

  7. The long version number is 1.3.1-25-g6e49f85f20. 

  8. This is compiled with configuration


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

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

  10. 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

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

    ```bash 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 

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

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

  13. 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

  14. 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 \

  15. 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. 

  16. 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. 

  17. 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

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

  19. locuszoom

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

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

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

  22. 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 ..

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

  24. It requires CentOS 8 (icelake, or login-q-*); otherwise it fails with message: GLIBC_2.18 not found.

    Upon installation, we supplement jupyter (python3 -m pip install jupyter –target=${PWD}/python; set PYTHONPATH in the module) and knitr (R_LIBS is set in the module). Furthermore, to allow for generality, python and R directories are symbollically linked.

    To enable rmarkdown, we need to get around issue of no Internet on icelake with the following,

    packages <- c("base64enc","bslib","cachem","cli","digest",

    somewhat repetitive nonetheless successful since some are package dependencies.

    $ quarto check

    [✓] Checking versions of quarto binary dependencies...
          Pandoc version 3.1.1: OK
          Dart Sass version 1.55.0: OK
    [✓] Checking versions of quarto dependencies......OK
    [✓] Checking Quarto installation......OK
          Version: 1.3.450
          Path: /usr/local/Cluster-Apps/ceuadmin/quarto/1.3.450-icelake/bin
    [✓] Checking basic markdown render....OK
    [✓] Checking Python 3 installation....OK
          Version: 3.8.11
          Path: /usr/local/software/spack/spack-views/rhel8-icelake-20211027_2/python-3.8.11/gcc-11.2.0/pqdmnzmwkrtp4e3gjibmcxho7g6ekpat/bin/python3
          Jupyter: 5.3.1
          Kernels: python3
    [✓] Checking Jupyter engine render....OK
    [✓] Checking R installation...........OK
          Version: 4.3.1
          Path: /usr/local/Cluster-Apps/R/4.3.1-icelake/lib64/R
            - /usr/local/Cluster-Apps/ceuadmin/quarto/R
            - /usr/local/Cluster-Apps/R/4.3.1-icelake/lib64/R/library
            - /rds/project/jmmh2/rds-jmmh2-public_databases/software/R
            - /rds/project/jmmh2/rds-jmmh2-public_databases/software/R-4.3.1/library
          knitr: 1.43
          rmarkdown: 2.23
    [✓] Checking Knitr engine render......OK

  25. 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

  26. 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

  27. 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 ..

  28. 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:


  29. The Python dependencies are set up as follows,

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

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

  30. It also includes gdc_dtt-ui 1.0.0