A full of ceuadmin modules

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. ↩

GUI

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

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.

↩

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

↩

Alternative site

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

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. ↩

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

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. ↩

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

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

↩

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 ↩

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

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

↩

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

↩

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

↩

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. ↩

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

↩

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. ↩

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

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

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

↩

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

↩

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

↩

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

↩

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. ↩

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 ..

↩

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. ↩

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 ↩

It also includes gdc_dtt-ui 1.0.0 ↩