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 \

module load ceuadmin/proj/6.3.0
module load ceuadmin/jasper/4.2.4
module load libxml2/2.9.13/gcc/fww2yzpt
module load ceuadmin/json-c/0.17-20230812-icelake
wget -qO- https://github.com/OSGeo/gdal/archive/refs/tags/v3.0.4.tar.gz | \
tar xvfz -
cd gdal-3.0.4/gdal
./configure --prefix=$CEUADMIN/gdal/3.0.4 --with-libjson-c=$CEUADMIN/json-c/0.17-20230812-icelake \
            --with-proj=/usr/local/Cluster-Apps/ceuadmin/proj/6.3.0 \
            --without-sqlite3
make

./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=$CEUADMIN/openssl/3.2.1-icelake --openssldir=$CEUADMIN/openssl/3.2.1-icelake/ssl
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=$CEUADMIN/openssl/1.1.1b-icelake --openssldir=$CEUADMIN/openssl/1.1.1b-icelake/ssl
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

wget -qO-  https://sourceware.org/ftp/lvm2/LVM2.2.03.23.tgz | \
tar xvfz -
cd LVM2.2.03.23
./configure --prefix=$CEUAMIN/LVM2/2.03.23-icelake --with-vdo=none
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

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}

cd /usr/local/Cluster-Apps/ceuadmin/dotnet/6.0.423
dotnet new tool-manifest
dotnet tool install paket
dotnet paket
dotnet paket add Mono.Unix --version 7.1.0-final.1.21458.1
```

The last line above is for OpenMS. We see `.config/dotnet-tools.json` and also

```
Paket version 8.0.3+75b30cdcb8859e8d129f139444d9b9b600bfff07
Adding package 'Mono.Unix' 7.1.0-final.1.21458.1
Resolving dependency graph...
 - Mono.Unix is pinned to 7.1.0-final.1.21458.1
Updated packages:
  Group: Main
    - Mono.Unix: 7.1.0-final.1.21458.1 (added)
Created dependency graph (1 packages in total)
Downloading Mono.Unix 7.1.0-final.1.21458.1
Download of Mono.Unix 7.1.0-final.1.21458.1 done in 249 milliseconds. (231504 kbit/s, 6 MB)
 - Project GenerateDeps.proj needs to be restored
Resolved package 'Mono.Unix' to version 7.1.0-final.1.21458.1
Total time taken: 3 seconds
```

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

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- https://github.com/jasper-software/jasper/archive/version-4.2.4/jasper-4.2.4.tar.gz | \
tar -xvzf -
module load texlive
cd jasper-version-4.2.4/build && ./build_all
ll ../tmp_cmake/release-1 -rt

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 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

export CARGO_HOME="$CEUADMIN/rust/nightly/cargo"
export RUSTUP_HOME="$CEUADMIN/rust/nightly/rustup"
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
export PATH="$CARGO_HOME/bin:$PATH"
rustup toolchain install nightly
rustup component add rust-src --toolchain nightly-x86_64-unknown-linux-gnu
rustup default nightly
rustc --version

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

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

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

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

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 install prefix=/usr/local/Cluster-Apps/ceuadmin/RSEM/1.3.3
make clean

wget -qO- https://github.com/dm-vdo/vdo/archive/refs/tags/8.3.1.1.tar.gz | \
tar xfz -
cd vdo-8.3.1.1/
make
make install DESTDIR=$CEUADMIN/vdo/8.3.1.1 INSTALLOWNER= defaultdocdir= defaultlicensedir=
# LVM2 as above but also into vdo/8.3.1.1
module load ceuadmin/vdo
cd LVM2.2.03.23
./configure --prefix=$CEUADMIN/LVM2/2.03.23-icelake
make
make install

wget -qO- https://github.com/microsoft/edit/archive/refs/tags/v1.0.0.tar.gz | \
tar xfz -
cd edit-1.0.0/
RUST_BACKTRACE=1
cargo build --config .cargo/release.toml --release

wget https://www.sqlite.org/2025/sqlite-src-3490200.zip
unzip sqlite-src-3490200.zip
cd sqlite-src-3490200
./configure --enable-all --prefix=$CEUADMIN/sqlite/3.49.2  TCLLIBDIR=$CEUADMIN/sqlite/3.49.2/tcl8.6
make && make install

wget -qO- https://github.com/Zettlr/Zettlr/releases/download/v3.5.1/Zettlr-3.5.1-x86_64.rpm | \
rpm2cpio - | \
cpio -idmv
wget https://github.com/retorquere/zotero-better-bibtex/releases/download/v6.7.269/zotero6-better-bibtex-6.7.269.xpi

wget -qO- https://github.com/Martinsos/edlib/archive/refs/tags/v1.2.7.tar.gz | tar tvfz -
cd edlib-1.2.7/
source ~/rds/software/py38/bin/activate
make

module load ceuadmin/Miniconda3/22.9.0
mkdir SVanalyzer
cd SVanalyzer/
conda create -n 0.36
conda activate 0.36
conda install -c bioconda svanalyzer
svanalyzer benchmark

tar xvfz /home/jhz22/.cpan/sources/authors/id/E/ET/ETJ/Log-Log4perl-1.57.tar.gz
cd Log-Log4perl-1.57/
export PERL5LIB=/usr/local/Cluster-Apps/ceuadmin/lib/perl5
make install
perl Makefile.PL INSTALL_BASE=$PERL5LIB
make
make install

wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz
wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz.tbi
wget ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.bed
truvari bench --base HG002_SVs_Tier1_v0.6.vcf.gz \
              --comp HG002_PacBio-HiFi-Revio_20231031_48x_GRCh38-GIABv3.vcf.gz \
              --reference GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta.gz \
              --includebed HG002_SVs_Tier1_v0.6.bed \
              --output truvari_HG002_bench \
              --giabreport --passonly --multimatch --refdist 2000 --chunksize 2000 --pctsize 0.70 --pctovl 0.0

wget https://github.com/RealTimeGenomics/rtg-tools/releases/download/3.13/rtg-tools-3.13-linux-x64.zip
unzip rtg-tools-3.13-linux-x64.zip
cd benchmarking
FA=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
SDF=GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.sdf
rtg format -o "$SDF" "$FA"

cd ~/rsd/software
mkdir fly && cd fly
ln -s /rds/project/rds-4o5vpvAowP0/software/fly ~/.fly
curl -L https://fly.io/install.sh | sh
export FLYCTL_INSTALL=~/.fly
export PATH="$FLYCTL_INSTALL/bin:$PATH"
flyctl --help
flyctl version
fly volumes create coffeeshop_vol --size 1
fly deploy

wget -qO- https://update.code.visualstudio.com/latest/linux-x64/stable | \
tar -xzf -
cd VSCode-linux-x64
./code

export UV_TOOL_DIR=$CEUADMIN/llm/0.26
uv tool install llm
uv tool dir

cat mutated_rCRS.fa | simLibrary -x 5 -r 150 --seed 12 > chrM_mut_5x.fasta
cat wide_rCRS.fa | simLibrary-x 4995 -r 150 --seed 12 > chrM_wide_4995x.fasta
cat chrM_mut_5x.fasta chrM_wide_4995x.fasta > chrM_sim_5000x_mut5x.fasta
simNGS -p "paired" -O "chrM_sim_5000x_mut5x_PE150" -o "fastq" -s 12 runfile chrM_sim_5000x_mut5x.fasta

wget -qO- https://github.com/clibs/cmocka/archive/refs/tags/1.1.5.tar.gz | tar xvfz -
cd cmocka-1.1.5
cmake -DUNIT_TESTING=ON -DCMAKE_INSTALL_PREFIX=$CEUADMIN/cmocka/1.1.5 -DCMAKE_BUILD_TYPE=Release ..
make
make install

wget -qO- https://github.com/sclorg/scl-utils/archive/refs/tags/2.0.3.tar.gz | tar xvfz -
cd scl-utils-2.0.3
mkdir build && cd build
cmake -DCMAKE_INSTALL_PREFIX=$CEUADMIN/scl-utils/2.0.3 -DCMAKE_BUILD_TYPE=Release ..
# cp mocka.h from mocka/1.1.5/include to tests; add several #include <below> to it; and #inlude "cmocka.h" from test_scllib.c
#include <stdarg.h>
#include <stddef.h>
#include <stdint.h>
#include <setjmp.h>
module load cmocka/1.1.5
make
make staging
# handling system folders
make install DESTDIR=staging
cd staging
mv usr/local/Cluster-Apps/ceuadmin/scl-utils/2.0.3/*
rm -rf usr
cp -r * $CEUADMIN/scl-utils/2.0.3

module load ceuadmin/leptonica/1.85.0
wget -qO- https://github.com/agl/jbig2enc/archive/refs/tags/0.30.tar.gz | tar xvfz -
cd jbig2enc-0.30/src
ln -s $INCLUDE/loptonica
cd -
module load ceuadmin/autoconf/2.72c.24-8e728
./autogen.sh
./configure --prefix=$CEUADMIN/jbig2enc/0.30
make
make install

wget -qO- https://pngquant.org/pngquant-linux.tar.bz2 | tar xjf -

wget https://mirrors.kernel.org/gcc/gcc-12.1.0/gcc-12.1.0.tar.xz
tar xf gcc-12.1.0.tar.xz
cd gcc-12.1.0
./contrib/download_prerequisites
mkdir ../gcc-build
cd ../gcc-build
../gcc-12.1.0/configure --prefix=$CEUADMIN/gcc/12.1.0 \
  --disable-multilib \
  --enable-languages=c,c++ \
  --disable-bootstrap \
  --disable-libssp \
  --disable-libquadmath \
  --disable-libvtv \
  --disable-libsanitizer
module load gettext/0.21/gcc/qnrcglqo
make -j5

wget https://github.com/WebAssembly/wasi-sdk/releases/download/wasi-sdk-20/wasi-sdk-20.0-linux.tar.gz
tar -xzf wasi-sdk-20.0-linux.tar.gz

module load ceuadmin/autoconf
wget -qO- https://github.com/NixOS/patchelf/releases/download/0.18.0/patchelf-0.18.0-x86_64.tar.gz | \
tar -xzf -
cd patchelf-0.18.0
./bootstrap.sh
./configure --prefix=$CEUADMIN/patchelf/0.18.0
make -j4
make install

wget -qO- https://kojipkgs.fedoraproject.org/packages/glibc/2.30/5.fc31/x86_64/glibc-2.30-5.fc31.x86_64.rpm | \
mkdir glibc-2.30-5
cd glibc-2.30-5/
rpm2cpio ../glibc-2.30-5.fc31.x86_64.rpm | cpio -idmv