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

singularity pull tensorflow_latest_gpu.sif docker://tensorflow/tensorflow:latest-gpu
singularity build --sandbox tensorflow docker://tensorflow/tensorflow:latest-gpu
singularity run tensorflow
python -c '
from tensorflow.python.client import device_lib
print(device_lib.list_local_devices())
'

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

singularity build crux.sif crux.def
singularity run crux.sif

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
wget https://github.com/docker/compose/releases/download/v2.36.0/docker-compose-linux-x86_64 -O docker-compose
chmod +x docker-compose

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"

ln -s src/src/test/resources test
java -Xmx4000M -jar MSGFPlus.jar -s test/test.mgf -o test/test.mzid \
     -d test/BSA.fasta -t 10ppm -m 0 -inst 1 -e 1 -ti -1,2 -ntt 1 -tda 1 -minLength 6 \
     -maxLength 50 -n 1 -thread 7 -mod test/Mods.txt
java -Xmx4000M -jar MSGFPlus.jar -s test/test.mgf -o test/test.mzid \
     -d  test/BSA.fasta -conf test/MSGFDB_Param.txt

source /usr/local/Cluster-Apps/ceuadmin/Anaconda3/2023.09-0/bin/activate
pip install git+https://github.com/grosenberger/easypqp.git@master

wget -qO- wget https://curl.se/download/curl-7.85.0.tar.gz | \
tar xfz -
cd curl-7.85.0/
module load ceuadmin/openssl/3.2.1
configure --prefix=$CEUADMIN/curl/7.85.0 --with-openssl
make
make install

wget -qO- https://github.com/libjpeg-turbo/libjpeg-turbo/archive/refs/tags/3.0.4.tar.gz | \
tar xvfz -
cd libjpeg-turbo-3.0.4/
mkdir build
cd build
cmake -G"Unix Makefiles" -DCMAKE_INSTALL_PREFIX=$CEUADMIN/libjpeg-turbo/3.0.4 ..
make
make install

module load ceuadmin/autoconf/2.72c.24-8e728
module load ceuadmin/proj/7.2.1
module load ceuadmin/libjpeg-turbo/3.0.4
module load zlib/1.2.11
wget -qO- https://github.com/OSGeo/libgeotiff/archive/refs/tags/1.7.3.tar.gz | \
tar xvfz -
cd libgeotiff-1.7.3/
cd libgeotiff
autoupdate
autogen.sh
configure --prefix=$CEUADMIN/libgeotiff/1.7.3 \
          --with-jpeg=$CEUADMIN/libjpeg-turbo/3.0.4 \
          --with-libtiff=$CEUADMIN/tiff/4.6.0 \
          --with-proj=$CEUADMIN/proj/7.2.1 \
          --with-zlib=/usr/local/Cluster-Apps/zlib/1.2.11
make -j3
make check
make install

wget -qO- https://github.com/OSGeo/gdal/releases/download/v3.7.0/gdal-3.7.0.tar.gz | \
tar xvfz -
cd gdal-3.7.0
mkdir build && cd build

module load ceuadmin/curl/7.85.0
module load ceuadmin/libiconv/1.17
module load ceuadmin/libarchive/3.7.5
module load ceuadmin/libgeotiff/1.7.3
module load ceuadmin/libjpeg-turbo/3.0.4
module load ceuadmin/libpng/1.5.30
module load ceuadmin/openssl/3.2.1
module load ceuadmin/poppler/0.84.0
module load ceuadmin/tiff/4.6.0

cmake -DGDAL_ENABLE_CURL=ON \
      -DGDAL_ENABLE_OGR=ON \
      -DGDAL_ENABLE_LIBARCHIVE=ON \
      -DGDAL_ENABLE_OPENSSL=ON \
      -DCMAKE_INSTALL_PREFIX=$CEUADMIN/gdal/3.7.0 \
      -DCURL_INCLUDE_DIR=$CEUADMIN/curl/7.85.0/include \
      -DCURL_LIBRARY_RELEASE=$CEUADMIN/curl/7.85.0/lib/libcurl.so \
      -DGEOTIFF_INCLUDE_DIR=$CEUADMIN/libgeotiff/1.7.3/include \
      -DGEOTIFF_LIBRARY_RELEASE=$CEUADMIN/libgeotiff/1.7.3/lib/libgeotiff.so \
      -DARCHIVE_INCLUDE_DIR=$CEUADMIN/libarchive/3.7.5/include \
      -DARCHIVE_LIBRARY=$CEUADMIN/libarchive/3.7.5/lib/libarchive.so \
      -DCRYPTOPP_INCLUDE_DIR=$CEUADMIN/cryptopp/8.9.0/include \
      -DCRYPTOPP_LIBRARY_RELEASE=$CEUADMIN/cryptopp/8.9.0/lib/libcryptopp.so \
      -DIconv_INCLUDE_DIR=$CEUADMIN/libiconv/1.17/include \
      -DIconv_LIBRARY=$CEUADMIN/libiconv/1.17/lib/libiconv.so \
      -DJPEG_INCLUDE_DIR=$CEUADMIN/libjpeg-turbo/3.0.4/include \
      -DJPEG_LIBRARY_RELEASE=$CEUADMIN/libjpeg-turbo/3.0.4/lib64/libjpeg.so \
      -DOPENSSL_INCLUDE_DIR=$CEUADMIN/openssl/3.2.1/include \
      -DOPENSSL_CRYPTO_LIBRARY=$CEUADMIN/openssl/3.2.1/lib/libcrypto.so \
      -DOPENSSL_SSL_LIBRARY=$CEUADMIN/openssl/3.2.1/lib/libssl.so \
      -DPNG_PNG_INCLUDE_DIR=$CEUADMIN/libpng/1.5.30/include \
      -DPNG_LIBRARY_RELEAS=$CEUADMIN/libpng/1.5.30/lib \
      -DPoppler_INCLUDE_DIR=$CEUADMIN//poppler/0.84.0/include \
      -DPoppler_LIBRARY=$CEUADMIN/poppler/0.84.0/lib64/libpoppler.so \
      -DPROJ_LIBRARY=$CEUADMIN/proj/7.2.1/lib/libproj.so \
      -DPROJ_INCLUDE_DIR=$CEUADMIN/proj/7.2.1/include \
      -DTIFF_LIBRARY=$CEUADMIN/tiff/4.6.0/lib/libtiff.so \
      -DTIFF_INCLUDE_DIR=$CEUADMIN/tiff/4.6.0/include \
      ..
make
module load ceuadmin/Anaconda3/2023.09-0
pip install rasterio
pip install geopandas
pip install gdal==3.7.0

wget -qO- https://github.com/nodejs/node/archive/refs/tags/v18.20.5.tar.gz | \
tar xvfz -
cd node-18.20.5
./configure --prefix=$CEUADMIN/node/18.20.5
make

curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.5/install.sh | bash
rm -rf ~/.npm
nvm install 18
nvm use 18
source ~/.bashrc
nvm use --delete-prefix v18.20.6
node -v
npm -v
npm install -g @marp-team/marp-cli puppeteer-core puppeteer
npm list -g @marp-team/marp-cli
npm cache clean --force

nvm install --lts
nvm use --lts
marp gaaw2.md

cd ~
curl -L https://www.npmjs.com/install.sh | sh

module load ceuadmin/node
npm install -g codedown

wget https://dl.google.com/linux/direct/google-chrome-stable_current_x86_64.rpm
rpm2cpio google-chrome-stable_current_x86_64.rpm | cpio -idmv

wget -qO- https://github.com/google/brotli/archive/refs/tags/v1.1.0.tar.gz | \
tar xfz -
cd brotli-1.1.0
mkdir build && cd build
cmake -DCMAKE_INSTALL_PREFIX=${CEUADMIN}/brotli/1.1.0 ..
make
make install

wget -qO- https://gnupg.org/ftp/gcrypt/libgcrypt/libgcrypt-1.5.3.tar.bz2 | x
tar xjf -
mv libgcrypt-1.5.3/ src
cd src
./configure --prefix=$CEUADMIN/libgcrypt/1.5.3
make
make install

wget -qO- https://ftp.gnu.org/gnu/texinfo/texinfo-7.2.tar.xz | \
tar Jxf -
mv texinfo-7.2/ src
cd src
make && make install

curl -L https://ollama.com/download/ollama-linux-amd64.tgz | \
tar xvfz -
ollama --help
ollama serve &
ollama list

module load ceuadmin/leptonica/1.85.0
module load ceuadmin/libgcrypt
module load ceuadmin/autoconf
wget -qO- https://github.com/tesseract-ocr/tesseract/archive/refs/tags/5.5.0.tar.gz | \
tar xvfz -
cd tesseract-5.5.0/
./autogen.sh
./configure --prefix=$CEUADMIN/tesseract/5.5.0 CXXFLAGS="-std=c++17" LDFLAGS="-lstdc++fs"
make && make install

wget -qO- https://github.com/tesseract-ocr/tessdata_best/archive/refs/tags/4.1.0.tar.gz | \
tar xvfz -
export TESSDATA_PREFIX="/usr/local/Cluster-Apps/ceuadmin/tesseract/5.5.0/share/tessdata_best-4.1.0"
tesseract --list-langs
tesseract lang.jpeg lang -l eng

wget https://file-assets.apidog.com/download/Apidog-linux-latest.zip
unzip  Apidog-linux-latest.zip
./Apidog.AppImage  --appimage-extract
./apidog --no-sandbox --help

https://repo.anaconda.com/archive/Anaconda3-2024.10-1-Linux-x86_64.sh
PREFIX=/usr/local/Cluster-Apps/ceuadmin/Anaconda3/2024.10-1
conda config --set auto_activate_base false

source /rds/project/rds-4o5vpvAowP0/software/Anaconda3-2024.10-1/bin/activate
conda create --name new_env python=3.9
conda activate new_env
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda install -c openms pyopenms --yes

export dst=/rds/project/rds-4o5vpvAowP0/software/micromamba/2.0.7
mkdir -p $dst && cd $dst
curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | \
tar -xvj bin/micromamba
export MAMBA_ROOT_PREFIX=$dst
eval "$(./bin/micromamba shell hook -s posix)"
micromamba activate
micromamba install python=3.13 jupyter -c conda-forge
export MAMBA_ROOT_PREFIX=$CEUADMIN/micromamba/2.0.7
mkdir $CEUADMIN/micromamba
ln -sf $dst $CEUADMIN/micromamba/2.0.7
# current shell
eval "$(micromamba shell hook --shell bash)"
micromamba activate
micromamba deactivate

micromamba create -n micromamba xtensor -c conda-forge
micromamba activate micromamba
micromamba config append channels conda-forge
micromamba config set channel_priority strict

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

# Initially, we build from GitHub
git clone https://github.com/ggerganov/llama.cpp.git
cd llama.cpp
mkdir build && cd build
cmake -DCMAKE_INSTALL_PREFIX=$CEUADMIN/llama.cpp/b4991 ..
make && make install
# It is recommended to build from release to avoid possible intermediate updates
wget -qO- https://github.com/ggml-org/llama.cpp/archive/refs/tags/b5303.tar.gz | tar xvfz -
cd llama.cpp-b5303/
mkdir build && cd build
cmake -DCMAKE_INSTALL_PREFIX=$CEUADMIN/llama.cpp/b5303 ..
make && make install

wget https://huggingface.co/unsloth/DeepSeek-V3-0324-GGUF/resolve/main/UD-IQ2_XXS/DeepSeek-V3-0324-UD-IQ2_XXS-00001-of-00005.gguf
wget https://huggingface.co/unsloth/DeepSeek-V3-0324-GGUF/resolve/main/UD-IQ2_XXS/DeepSeek-V3-0324-UD-IQ2_XXS-00002-of-00005.gguf
wget https://huggingface.co/unsloth/DeepSeek-V3-0324-GGUF/resolve/main/UD-IQ2_XXS/DeepSeek-V3-0324-UD-IQ2_XXS-00003-of-00005.gguf
wget https://huggingface.co/unsloth/DeepSeek-V3-0324-GGUF/resolve/main/UD-IQ2_XXS/DeepSeek-V3-0324-UD-IQ2_XXS-00004-of-00005.gguf
wget https://huggingface.co/unsloth/DeepSeek-V3-0324-GGUF/resolve/main/UD-IQ2_XXS/DeepSeek-V3-0324-UD-IQ2_XXS-00005-of-00005.gguf
module load ceuadmin/llama.cpp
llama-gguf-split --merge DeepSeek-V3-0324-UD-IQ2_XXS-00001-of-00005.gguf DeepSeek-V3-0324-UD-IQ2_XXS.gguf

module load python/3.11.0-icl
python -m venv InstaNovo
source InstaNovo/bin/activate
pip install "instanovo"
instanovo version
instanovo predict --data-path=sample_data/*mgf --output-path=sample_data/spectra.csv

singularity exec tensorflow/ /usr/local/bin/instanovo version
singularity exec tensorflow/ /usr/local/bin/instanovo predict --data-path=InstaNovo/src/sample_data/*.mgf --output-path=spectra.csv
singularity build instanovo-1.1.1.sif tensorflow/
singularity run instanovo-1.1.1.sif /usr/local/bin/instanovo predict --data-path=sample_data/*mgf --output-path=new.csv

git clone https://github.com/instadeepai/InstaNovo.git
cd InstaNovo
module load ceuadmin/uv/0.6.14
uv sync --extra cpu
uv run pre-commit install
source .venv/bin/activate
instanovo predict --data-path=sample_data/*mgf --output-path=spectrum.csv

module load python/3.11.0-icl
python -m venv scGPT-models
source scGPT-models/bin/activate
pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu117
pip install packaging
pip install ipykernel
pip install scgpt flash-attn==1.0.4
pip uninstall numpy -y
pip install numpy==1.25.2
pip install scvi-tools==0.20.3 anndata==0.9.2 scanpy==1.9.3
pip install wandb
pip install faiss-cpu
pip install nbformat
pip list | awk '/scanpy|scib|scvi|scgpt|flash-attn|torch|wandb/'

module load python/3.9.12/gcc/pdcqf4o5
python -m venv scGPT-release
source scGPT-release/bin/activate
wget -qO- https://github.com/bowang-lab/scGPT/archive/refs/tags/v0.2.4.tar.gz | tar xvfz -
cd scGPT-0.2.4/
pip install -e .
pip install ipykernel
pip install gseapy
pip install torch.geometric
pip install einops
pip list
pip uninstall torch -y
pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu117
pip install flash-attn==1.0.4
pip uninstall numpy -y
pip install numpy==1.25.2
pip install wandb
pip install iprogress
pip install nbformat
pip list | awk '/scanpy|scib|scvi|scgpt|flash-attn|torch|wandb/'

pip uninstall scanpy -y
pip install scanpy
pip list | grep scanpy

module load python/3.9.12/gcc/pdcqf4o5
python -m venv drugassist
source drugassist/bin/activate
pip install --upgrade pip
git clone https://github.com/blazerye/DrugAssist.git
cd DrugAssist
pip install packaging
pip install torch==2.0.1
pip install scipy==1.8.0
sed -i '/torch/d;s/^scipy==.*$/scipy==1.8.0/' requirements.txt
pip install -r requirements.txt
huggingface-cli login

export HF_DATASETS_CACHE=~/.cache/huggingface/datasets/
python <<END
from datasets import load_dataset

# Login using e.g. `huggingface-cli login` to access this dataset
ds = load_dataset("blazerye/MolOpt-Instructions")
END

# It only supports GPUs
sh run_sft_lora.sh

curl -LsSf https://astral.sh/uv/install.sh | sh

git clone --recursive https://github.com/microsoft/BitNet.git b1.58-2B-4T
cd b1.58-2B-4T/
module load python/3.9.12/gcc/pdcqf4o5
python -m venv BitNet
source BitNet/bin/activate
pip install -r requirements.txt
huggingface-cli download microsoft/BitNet-b1.58-2B-4T-gguf --local-dir models/BitNet-b1.58-2B-4T
python setup_env.py -md models/BitNet-b1.58-2B-4T -q i2_s
python run_inference.py -m models/BitNet-b1.58-2B-4T/ggml-model-i2_s.gguf -p "You are a helpful assistant" -cnv

module load ceuadmin/BitNet
run_inference -p "In this chapter, we'll discuss first steps with generative AI in Python."
run_inference -p "Write an essay about precision medicine" -n 900 -t 8
run_inference -p "Why the sky is blue" -n 900 -t 1

git clone https://github.com/vandijklab/cell2sentence.git
cd cell2sentence/
module load python/3.9.12/gcc/pdcqf4o5
python -m venv cell2sentence
source cell2sentence/bin/activate
make install
pip install flash-attn==1.0.4 --no-build-isolation

git clone https://github.com/sriramlab/GENIE.git
cd GENIE
git checkout v1.1.1
mkdir 1.1.1 && cd 1.1.1
cmake ..
make

#!/usr/bin/bash
module load ceuadmin/PGS-CSx
python ${PGS_CSx_ROOT}/PRScsx.py
       --ref_dir=${LD_UKBB} \
       --bim_prefix=test_data/test \
       --sst_file=test_data/EUR_sumstats.txt,test_data/EAS_sumstats.txt \
       --n_gwas=200000,100000 \
       --pop=EUR,EAS \
       --chrom=22 \
       --phi=1e-2 \
       --out_dir=. \
       --out_name=test

make
make install
make clean