A. Setup of modules

module load openblas/0.2.15
make

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 ..

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}

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

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 \

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

curl -sSL https://cache.ruby-lang.org/pub/ruby/2.7/ruby-2.7.5.tar.gz -o ruby-2.7.5.tar.gz
tar -xzf ruby-2.7.5.tar.gz
cd ruby-2.7.5
./configure --prefix=$CEUADMIN/ruby/2.7.5
make
make install
rvm reset

./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

./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

module load gettext/0.21/gcc/qnrcglqo
configure --prefix=$CEUADMIN/gnutls/3.8.4-icelake --with-included-unistring
make
make install

 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

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

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

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

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

curl -fsSL get.nextflow.io | bash

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

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

nextflow run pgscatalog/pgsc_calc -profile test,singularity

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

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

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

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

configure --prefix=$CEUADMIN/openssh/9.7p1-icelake
make
make install

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

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

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

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

make device-mapper
make install_device-mapper

# 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

configure --prefix=$CEUADMIN/krb5/1.21.2-icelake
module load gettext/0.21/gcc/qnrcglqo
make install

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

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

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")'

cd /rds/project/jmmh2/rds-jmmh2-public_databases/software
wget https://github.com/spyder-ide/spyder/releases/download/v5.5.4/EXPERIMENTAL-Spyder-5.5.4-Linux-x86_64.sh
bash EXPERIMENTAL-Spyder-5.5.4-Linux-x86_64.sh

git clone https://github.com/crux-toolkit && cd crux-toolkit
export PERL5LIB=
module load ceuadmin/openssh/9.7p1-icelake \
            ceuadmin/openssl/3.2.1-icelake \
            ceuadmin/libssh/0.10.6-icelake \
            ceuadmin/boost/1.76.0 \
            ceuadmin/krb5/1.21.2-icelake ceuadmin/p7zip-zstd/17.05
cmake .
make

docker pull chambm/pwiz-skyline-i-agree-to-the-vendor-licenses
docker run -it --rm chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine msconvert --help
docker run -it --rm chambm/pwiz-skyline-i-agree-to-the-vendor-licenses wine SkylineCmd --help
docker run -it --rm -e WINEDEBUG=-all -v /your/data:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses \
       wine msconvert /data/file.raw

docker run -it --rm -e WINEDEBUG=-all -v /home/jhz22/D/Downloads:/data chambm/pwiz-skyline-i-agree-to-the-vendor-licenses \                                                                  
       wine msconvert /data/szwk901104i19801xms1.raw --filter "peakPicking true 1-"

module load python/3.8.11/gcc/pqdmnzmw
wget -qO- http://sourceforge.net/projects/boost/files/boost/1.76.0/boost_1_76_0.tar.gz | \
tar xvzf -
cd boost_1_76_0
./bootstrap.sh
./b2 --prefix=$CEUADMIN/boost/1.76.0 install
./bjam --with-regex --with-filesystem --with-iostreams --with-thread --with-program_options \
        --with-serialization --with-system --with-date_time install
export BOOST_ROOT=/usr/local/src/boost_1_76_0

module load ceuadmin/krb5/1.21.2-icelake
configure --prefix=${CEUADMIN}/wine/8.21 --enable-win64
make install

#!/usr/bin/bash

export fasta=~/rds/public_databases/UniProt/uniref100.fasta.gz
export fasta=~/rds/public_databases/UniProt/uniprot_sprot.fasta.gz
export regions=UP000005640_9606_proteome.bed

module load ceuadmin/seqkit
seqkit subseq --bed ${regions} --seq-type protein --out-file output.fasta ${fasta}

awk '{print $4}' ${regions} | sort | uniq > protein_ids.txt
seqkit grep -f protein_ids.txt ${fasta} > output.fasta

# A contrast with the genomic counterpart
# bedtools getfasta -fo output.fasta -s -fullHeader -fi ${fasta} -bed ${regions}

module load ceuadmin/FlashLFQ
flashlfq --idt MaxQuant/msms.txt --rep . --ppm 5 --chg

export folder=$CEUADMIN/docker/24.0.5
mkdir -p ${folder}
cd ${folder}
curl -fsSL https://download.docker.com/linux/static/stable/x86_64/docker-24.0.5.tgz -o docker.tgz
tar xzvf docker.tgz --strip 1
export PATH=${folder}:$PATH
export DOCKER_HOST=unix:///run/user/$(id -u)/docker.sock
# a normal run:
dockerd --experimental --rootless
systemctl --user enable docker
systemctl --user start docker
docker run hello-world

export mydocker=$CEUADMIN/docker/24.0.5
curl -fsSL https://raw.githubusercontent.com/docker/docker/master/contrib/dockerd-rootless-setuptool.sh \
     -o $mydocker/dockerd-rootless-setuptool.sh
chmod +x $mydocker/dockerd-rootless-setuptool.sh
curl -fsSL https://raw.githubusercontent.com/docker/docker/master/contrib/dockerd-rootless.sh \
     -o $mydocker/24.0.5/dockerd-rootless.sh
chmod +x $mydocker/dockerd-rootless.sh
wget -qO- https://github.com/rootless-containers/rootlesskit/releases/download/v2.1.0/rootlesskit-x86_64.tar.gz | \
tar xvfz -
echo "$USER:100000:65536" > ~/.subuid
echo "$USER:100000:65536" > ~/.subgid
export DOCKER_ROOTLESS_SUBUID=$(cat ~/.subuid)
export DOCKER_ROOTLESS_SUBGID=$(cat ~/.subgid)
${mydocker}/dockerd-rootless-setuptool.sh install

id -u
id -g

wget -qO- https://github.com/containers/podman/releases/download/v5.1.1/podman-remote-static-linux_amd64.tar.gz | tar xvfz -
cd bin
ln -s podman-remote-static-linux_amd64 podman
echo "$USER:100000:65536" > $HOME/.subuid
echo "$USER:100000:65536" > $HOME/.subgid
cd ..

# podman-helpers
mkdir podman-helpers && cd podman-helpers
wget https://github.com/containers/gvisor-tap-vsock/releases/download/v0.7.3/gvproxy-linux-amd64 -O gvproxy
chmod +x gvproxy
wget https://github.com/containers/fuse-overlayfs/releases/download/v1.14/fuse-overlayfs-x86_64
chmod +x fuse-overlayfs-x86_64
curl -o slirp4netns --fail -L https://github.com/rootless-containers/slirp4netns/releases/download/v1.3.1/slirp4netns-$(uname -m)
chmod +x slirp4netns
cd ..
# containers
mkdir containers
echo '[containers]' > containers/containers.conf
echo '[engine]' >> containers/containers.conf
echo 'helper_binaries_dir = "/home/jhz22/podman-helpers"' >> containers/containers.conf
echo 'events_logger = "file"' >> containers/containers.conf
ln -sf ${PWD}/containers $HOME/.config/containers
# podman
module load ceuadmin/qemu
pkill podman
podman system connection list
podman machine init
podman machine start
podman run quay.io/podman/hello
podman pull docker.io/library/hello-world
podman run --rm docker.io/library/hello-world
# additional notes
podman machine rm podman-machine-default
podman system connection add --default podman-machine-default ssh://core@127.0.0.1:39137/run/user/10024/podman/podman.sock

export prefix=$CEUADMIN/qemu/
export ENV_DIR=$prefix/venv
mkdir build && cd build
module load python/3.8.11/gcc/pqdmnzmw
python -m venv --system-site-packages ${ENV_DIR}
source $prefix/venv/bin/activate
pip install --prefix=${ENV_DIR} sphinx
pip install --prefix=${ENV_DIR} sphinx_rtd_theme==1.1.1
pip install --prefix=${ENV_DIR} ninja
wget -qO- https://download.qemu.org/qemu-9.0.1.tar.xz | \
tar vxJf -
cd qemu-9.0.1
module load ncurses/6.2/gcc/givuz2aq libidn2/2.3.0/gcc/ph36ygoa 
module load gettext/0.21/gcc/qnrcglqo
module load ceuadmin/gnutls/3.8.4-icelake ceuadmin/nettle/3.9-icelake ceuadmin/krb5/1.21.2-icelake
export gettext=/usr/local/software/spack/spack-views/rhel8-icelake-20211027_2/gettext-0.21/gcc-11.2.0/qnrcglqov5au2zv56tumhhf4n6mds34n
../configure --prefix=$prefix/9.0.1\
             --target-list=x86_64-softmmu \
             --extra-ldflags="-L4gettext -lintl" \
             --extra-cflags="-I$gettext/include"
make -j4
make install

export EXTRA_ARGS=${EXTRA_ARGS:-$@}
## Fedora CoreOS image for x86_64 (QEMU)
export PODMAN_X86_64_MACHINE_NAME=${PODMAN_X86_64_MACHINE_NAME:-x86_64}
export PODMAN_X86_64_MACHINE_NAME_EXISTS=$(podman machine list | grep ${PODMAN_X86_64_MACHINE_NAME} | wc -l | tr -d '[:space:]')
export PODMAN_QEMU_IMAGE="fedora-coreos-39.20231101.3.0-qemu.x86_64.qcow2.xz"
export DOWNLOAD_DIR=${DOWNLOAD_DIR:-.}
if [ ${PODMAN_X86_64_MACHINE_NAME_EXISTS} -lt 1 ]; then
    curl -C- -O "https://builds.coreos.fedoraproject.org/prod/streams/stable/builds/39.20231101.3.0/x86_64/${PODMAN_QEMU_IMAGE}"
    podman machine init --image ${DOWNLOAD_DIR}/${PODMAN_QEMU_IMAGE} ${PODMAN_X86_64_MACHINE_NAME} ${EXTRA_ARGS}
else
    echo "[Info] Machine ${PODMAN_X86_64_MACHINE_NAME} already exists. If you want to recreate it, run 'podman machine rm ${PODMAN_X86_64_MACHINE_NAME}'"
fi
podman machine list
lsmod
## TCG (Tiny Code Generator)
xz -d ${PODMAN_QEMU_IMAGE}
qemu-system-x86_64 -m 2048 -cpu qemu64 -smp 2 -drive file=fedora-coreos-39.20231101.3.0-qemu.x86_64.qcow2,format=qcow2 -accel tcg
## Change machine settings
### Get the machine config file name
machineConfigFile="$(podman machine inspect ${PODMAN_X86_64_MACHINE_NAME} | jq -r '.[].ConfigPath.Path')"
### https://docs.openstack.org/image-guide/obtain-images.html
wget https://cloud-images.ubuntu.com/noble/current/noble-server-cloudimg-amd64.img
qemu-system-x86_64 -m 2048 -cpu qemu64 -smp 2 -drive file=noble-server-cloudimg-amd64.img,format=qcow2 -accel tcg
### No GUI
qemu-system-x86_64 -m 2048 -cpu qemu64 -smp 2 -drive file=fedora-coreos-39.20231101.3.0-qemu.x86_64.qcow2,format=qcow2,cache=writeback -nographic

wget -qO- https://download.libguestfs.org/hivex/hivex-1.3.23.tar.gz | tar xfz -
cd hivex-1.3.23
module load ceuadmin/ocaml/4.14.2
module load ceuadmin/ruby/2.7.5
export PERLB5LIB=
autoreconf -i --force
./generator/generator.ml
./configure --prefix=$CEUADMIN/hivex/1.3.23
make
cd perl
perl Makefile.PL INSTALLDIRS=site INSTALL_BASE=/usr/local/Cluster-Apps/ceuadmin/hivex/1.3.23
cd ..
make
make install

wget -qO- http://download.camlcity.org/download/findlib-1.9.6.tar.gz | tar xfz -
cd findlib-1.9.6
configure -bindir $CEUADMIN/findlib/1.9.6/bin -mandir $CEUADMIN/findlib/1.9.6/man
make
make install

opam init
opam switch list
opam switch list-available
opam switch create ocaml-4.14
opam install -y hivex --destdir $CEUADMIN/hivex/1.3.23

wget -qO- https://download.libguestfs.org/1.52-stable/libguestfs-1.52.2.tar.gz | tar xfz -
cd libguestfs-1.52.2
./configure --prefix=$CEUADMIN/libguestfs/1.48.6 \
            --with-extra="findlib=$CEUADMIN/findlib/1.9.6" \
            --with-extra="hivex=$CEUADMIN/hivex/1.3.23"