Appendix A. 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 Generic
2022-11-06 libpng/0.5.30 Generic
"" libgit2/1.1.0 Generic11
"" 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 Generic12
"" gnutls/3.7.8 Generic13
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 Genetics14
"" 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 Generic15
"" 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*16
"" 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*17
"" 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 Generic18
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 Genetics19
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 Genetics20
2023-06-05 gsl/2.7.1 Generic
2023-06-06 allegre/2.0f Genetics
2023-06-14 autoconf/2.72c.24-8e728 Generic21
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 Generic22
2023-08-06 finemap/1.4.2 Genetics
2023-08-10 GreenAlgorithmsforHPC/0.3 Generic
2023-08-12 xpdf/4.04 Generic23
2023-08-22 thunderbird/115.1.1 Generic
2023-08-24 pdfjam/3.07 Generic
2023-09-03 2.0.0-pre1ge32bec Genetic24
"" spead-sheet-widget Generic
2023-09-27 ncbi-vdb/3.0.8 Genetics25
"" sra-tools/3.0.8 Genetics26
"" gatk/4.4.0.0 Genetics27
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 Genetics28
2023-12-13 rust/1.74.1 Generic
2023-12-20 verifyBamID/1.1.3 Genetics
2023-12-21 verifyBamID/2.0.1 Genetics29
2023-12-27 regtools/1.0.0 Genetics30
"" VarScan/2.4.6 Genetics31
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 Generic32
2024-01-19 htslib/1.19 Genetics
2024-01-23 nextflow/23.10.1 Generic33
"" go/1.21.6 Generic
"" singularity/4.0.3 Generic34
"" libseccomp/2.5.5 Generic
2024-01-24 fraposa_pgsc/0.1.0 Genetics35
"" pgsc_calc/2.0.0-alpha.4 Genetics36
2024-01-27 glibc/2.18 Generic
"" glibc/2.26 Generic
"" deno/1.40.2 Generic37
"" deno/1.40.2-icelake Generic
"" quarto/1.4.549 Generic
2024-02-29 R/4.3.3 Generic38
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 Generic39
"" automake/1.16.5 Generic40
"" 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 Generic41
"" openssh/9.7p1-icelake Generic42
2024-03-31 ensembl-vep/111-icelake Genetics43
2024-04-01 json-c/0.17-20230812-icelake Generic44
"" device-mapper/1.02.28-icelake Generic
"" LVM2/2.03.23-icelake Generic45
2024-04-02 cryptsetup/2.7.1-icelake Generic46
2024-04-05 krb5/1.21.2-icelake Generic47
"" git/1.44.0-icelake Generic48
"" openssl/1.1.1b-icelake Generic
"" libssh2/1.11.0-icelake Generic
"" libssh/0.10.6-icelake Generic
2024-04-22 peer/1.3 Generic49
2024-04-29 ImageMagick/7.1.1-31 Generic50
2024-05-15 rtmpdump/2.3 Generic51

* 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.

Word cloud diagrams

They are generated from the following script,

if [ "$(uname -n | sed 's/-[0-9]*$//')" == "login-p" ]; then
   module load ceuadmin/R
else
   module load ceuadmin/R/4.4.0-icelake
fi
grep -e Generic ${CEUADMIN}/doc/setup.md | grep "^[|]" | awk '{print $4}' > generic.lst
grep -e Genetics ${CEUADMIN}/doc/setup.md | grep "^[|]" | awk '{print $4}' > genetics.lst
grep -e Genetics -e Generic ${CEUADMIN}/doc/setup.md | grep "^[|]" | awk '{print $4}' | wc -l
rm -f ceuadmin.png generic.png genetics.png
Rscript -e '
  library(RColorBrewer)
  library(dplyr)
  library(tm)
  library(wordcloud)
  options(width=110);
  ceuadmin <- Sys.getenv("CEUADMIN")
  wc <- function(modules,png)
  {
    print(length(modules))
    docs <- Corpus(VectorSource(modules))
    m <- TermDocumentMatrix(docs) %>%
         as.matrix()
    words <- sort(rowSums(m),decreasing=TRUE)
    freq <- rpois(length(words),lambda=3)
    png(png,,res=300,height=10,width=10,units="in")
    wordcloud(names(words), freq, min.freq = 1, max.words=200, random.order=FALSE, rot.per=0.35, colors=brewer.pal(8, "Dark2"))
    dev.off()
  }
  set.seed(1234321)
  generic <- scan("generic.lst",what="")
  genetics <- scan("genetics.lst",what="")
  wc(generic,"generic.png")
  wc(genetics,"genetics.png")
  unlink(c("generic.lst","genetics.lst"))
  modules <- setdiff(dir(ceuadmin),c("doc","lib","misc","sources","generic.png","genetics.png"))
  wc(modules,"ceuadmin.png")
  print(modules)
'

Footnotes


  1. metal

    Notes on METAL 2020-05-05r

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

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

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

  2. gema

    Note on compiling from source

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

    module load openblas/0.2.15
    make
    

  3. fcgene

    Alternative site

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

  4. jq

    The executable points to the one available from the website.

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

  5. qtltools

    The long version number is 1.3.1-25-g6e49f85f20. 

  6. exiv2

    This is compiled with configuration

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

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

  7. libxslt

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

  8. libxml2

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

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

    The module file is expicitly appended with

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

  9. gdal

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

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

  10. expat

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

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

  11. 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
    

  12. 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
    

  13. gnutls

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

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

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

  14. 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. 

  15. 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
    

  16. OpenMS

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

  17. locuszoom

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

  18. 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. 

  19. pwcoco

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

  20. 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
    

  21. 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
    

  22. quarto

    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",
                  "ellipsis","evaluate","fastmap","fontawesome","fs",
                  "glue","htmltools","jquerylib","jsonlite","knitr",
                  "lifecycle","memoise","mime","R6","rappdirs",
                  "rlang","rmarkdown","sass","stringi","stringr",
                  "tinytex","vctrs","xfun","yaml")
    download.packages(packages,".")
    install.packages(dir(pattern="tar.gz"),lib="R",repos=NULL)
    

    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
          LibPaths:
            - /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
    

  23. 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
    

  24. pspp

    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

  25. ncbi-vdb

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

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

  26. sra-tools

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

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

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

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

  27. 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 

  28. gdc

    It also includes gdc_dtt-ui 1.0.0 

  29. 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. 

  30. regtools

    gcc/6 is required for C++11. 

  31. varscan

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

  32. tatami

    The following aspects are required.

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

  33. nextflow

    curl -fsSL get.nextflow.io | bash
    

  34. singularity

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

  35. fraposa

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

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

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

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

  36. 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. 

  37. 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
    

  38. R

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

  39. GitKraken

    This replaces 8.1.0. 

  40. automake

    This is required by pspp 2.0.0. 

  41. 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
    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
    make install
    

  42. 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. 

  43. ensembl-vep

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

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

    A log file is kept here.

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

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

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

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

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

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

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

    Our example data here is 442807041.vcf,

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

    and we run script,

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

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

  44. 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
    

  45. LVM2

    Only device mapper is installed, i.e.,

    make device-mapper
    make install_device-mapper
    

  46. 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
    

  47. krb5-icelake

    It is possible to use the default ssh.

     configure --prefix=$CEUADMIN/krb5/1.21.2-icelake
     make install
    

  48. 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

  49. peer

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

  50. 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
    

  51. rtmpdump

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

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