Software

Software-specific configurations can often be found from ~/.config and ~/.local or other .* locations such as .vscode.

ceuadmin

See https://cambridge-ceu.github.io/csd3/systems/ceuadmin.html for additional information.

git

The popular git can be loaded,

git --help
git add --help

libraOffice

Official website: https://www.libreoffice.org/

The executables (oocalc, ooffice, ooimpress, oomath, ooviewdoc, oowriter) are in the /usr/bin directory and can be conveniently called from the console, e.g.,

oowriter README.docx

to load the Word document.

MATLAB

Official website: https://www.mathworks.com/products/matlab.html.

module avail matlab
module load matlab/r2019b

followed by matlab.

MySQL

One could access databases elsewhere, e.g., at UCSC – see examples on VEP.

There isn't any MySQL cluster running as a general service on CSD3. Do you believe your group has something running on a VM hosted on our network possibly? If you need a database for your work, running it in your own department and then allowing access to it from CSD3. Databases are not suitable candidates to run on a HPC cluster, the resource requirements are different and by definition they need to be running continuously whilst access is required, so wouldn't be run via SLURM for example.

R

See languages section, https://cambridge-ceu.github.io/csd3/systems/languages.html.

pspp

Official website: https://www.gnu.org/software/pspp/

module load ceuadmin/pspp

with command-line tool pspp and a GUI counterpart psppire.

singularity

Web: https://docs.sylabs.io/ (User Guide)

Real applications in WES/WGS are given here, https://jinghuazhao.github.io/SCALLOP-Seq/NOTES/.

Similarly for MS experiment, the following is also from an ongoing project.

singularity --version
module load ceuadmin/pwiz/3_0_24163_9bfa69a-wine
export SIF=pwiz-skyline-i-agree-to-the-vendor-licenses_latest.sif
singularity pull --name ${SIF} docker://chambm/pwiz-skyline-i-agree-to-the-vendor-licenses
singularity exec --env WINEDEBUG=-all \
                  -B /rds/project/rds-MkfvQMuSUxk/interval/caprion_proteomics/spectral_library_ZWK/:/data \
                      ${SIF} \
                      wine msconvert /data/szwk901104i19901xms1.raw

where pull generates pwiz-skyline-i-agree-to-the-vendor-licenses_latest.sif at current directory.

See also https://docs.sylabs.io/guides/2.6/user-guide/singularity_and_docker.html.

An example is ready from diann.def for diann/2.0.2,

BootStrap: docker
From: ubuntu:22.04

%files
    diann-linux  /usr/local/bin/diann-linux
    libc10.so    /usr/lib/
    libgomp-98b21ff3.so.1  /usr/lib/
    libtimsdata.so  /usr/lib/
    libtorch_cpu.so  /usr/lib/
    libtorch.so  /usr/lib/

%post
    # Set timezone
    ln -fs /usr/share/zoneinfo/UTC /etc/localtime

    # Update package lists and install dependencies
    apt-get update
    apt-get install -y libgomp1 libstdc++6 libc6 locales

    # Configure locales
    locale-gen en_US.UTF-8
    echo "LANG=en_US.UTF-8" > /etc/locale.conf
    echo "LC_ALL=en_US.UTF-8" >> /etc/locale.conf

    # Clean up apt cache
    rm -rf /var/lib/apt/lists/*

    # Ensure diann-linux is executable and create a symlink
    chmod +x /usr/local/bin/diann-linux
    ln -sf /usr/local/bin/diann-linux /usr/local/bin/diann

%runscript
    exec /usr/local/bin/diann "$@"

%labels
    Author YourName
    Version 2.0.2
    Description "DiaNN container for proteomics analysis"

so we can proceed with

singularrity build diann.sif diann.def
singularity run diann.sif --fasta /path/to/human_proteome.fasta --dir /path/to/data/ --out output.txt

See https://www.bioconductor.org/help/docker/ on bioconductor.

SLURM

Due to increase of size, the entry is moved here, https://cambridge-ceu.github.io/csd3/systems/ParallelComputing.html.

Stata

Official website: https://www.stata.com/.

We issue module avail ceuadmin/stata to give,

----------------------------------------------------------------- /usr/local/Cluster-Config/modulefiles -----------------------------------------------------------------
ceuadmin/stata/14  ceuadmin/stata/15  ceuadmin/stata/16

e.g., as a CEU member the following is possible,

module load ceuadmin/stata/14

The meta-analysis (metan) and Mendelian Randomisation (mrrobust) packages can be installed as follows,

ssc install metan
net install mrrobust, from("https://raw.github.com/remlapmot/mrrobust/master/") replace

It is now also possible systemwide, with module avail stata giving

-------------------------------------------------- /usr/local/Cluster-Config/modulefiles --------------------------------------------------
stata/14 stata/17 stata/18

so as to use module load stata; stata