Install DeepSomatic r1.9 locally on your server without docker

Requirements

• ubuntu 22.04
• CPUs support SSE4 & AVX
• sudo privilege

Install

1. Download prebuilt DeepSomatic binaries
2. Download DeepSomatic models
3. Prepare environment for /usr/bin/python3 & DeepSomatic using apt
4. Prepare environment for DeepSomatic using run-prereq.sh
5. Install DeepSomatic requirements in /usr/bin/python3
6. Tensorflow CUDA issues

Download prebuilt DeepSomatic binaries

gsutil -m rsync -r "gs://deepvariant/binaries/DeepVariant/1.9.0/DeepVariant-1.9.0" .


# local directory
/t9k/mnt/WorkSpace/data/ngs/xuzhenyu/dv/DeepVariant-1.9.0

Download DeepSomatic models

# deepsomatic models
DEST="./models/deepsomatic/1.9.0/"
mkdir -p "${DEST}"

gsutil -m rsync -r \
  "gs://deepvariant/models/DeepSomatic/1.9.0/" \
  "${DEST}"


# local directory
/t9k/mnt/WorkSpace/data/ngs/xuzhenyu/dv/models

Prepare environment for /usr/bin/python3 & DeepSomatic using apt

sudo apt update
sudo apt install apt-utils build-essential python3-dev python3-pip python3-pip-whl \
  libcairo2-dev libgirepository1.0-dev pkg-config libdbus-1-dev parallel

Prepare environment for DeepSomatic using run-prereq.sh

bash run-prereq.sh


# local directory
bash dv_tf/run-prereq.sh

Install DeepSomatic requirements in /usr/bin/python3 or specified python 3.10

/usr/bin/python3 -m pip install -r requirements.txt --no-deps -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple


# or use whatever prepared python 3.10 you like
micromamba run -n tf pip install -r requirements.txt --no-deps -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple

Install DeepSomatic to /opt

Use sudo if needed

mkdir -p /opt/deepvariant/bin/deepsomatic/

# copy https://github.com/google/deepvariant/raw/refs/heads/r1.9/scripts/run_deepsomatic.py to /opt/deepvariant/bin/deepsomatic
cp /path/to/run_deepsomatic.py /opt/deepvariant/bin/deepsomatic/

# copy prebuilt binaries to /opt/deepvariant/bin
rsync -avP /path/to/deepvariant/binaries /opt/deepvariant/bin/
# if use customized python3 other than /usr/bin/python3, patch the binaries
# modify the BIN_DIR and PYTHON when needed
bash patch/patch_dv_stub.sh

# copy deepsomatic models to /opt/models/deepsomatic
mkdir -p /opt/models/deepsomatic
bash rsync_install_deepsomatic_models.sh

# generate command cli
bash make_cli.sh

Local shared directory

mkdir -p /opt/deepvariant/bin/deepsomatic/

# copy locally shared run_deepsomatic.py
cp /t9k/mnt/WorkSpace/data/ngs/xuzhenyu/dv/deepvariant/scripts/run_deepsomatic.py /opt/deepvariant/bin/deepsomatic/

# copy prebuilt binaries to /opt/deepvariant/bin
rsync -avP /t9k/mnt/WorkSpace/data/ngs/xuzhenyu/dv/DeepVariant-1.9.0/ /opt/deepvariant/bin/
# if use customized python3 other than /usr/bin/python3, patch the binaries
# modify the BIN_DIR and PYTHON when needed
bash patch/patch_dv_stub.sh

# copy deepsomatic models to /opt/models/deepsomatic
# remember to modify SRC_BASE path to /t9k/mnt/WorkSpace/data/ngs/xuzhenyu/dv/models/deepsomatic/1.9.0/savedmodels
mkdir -p /opt/models/deepsomatic
bash rsync_install_deepsomatic_models.sh

# generate command cli
# remember to modify PYTHON variables and 
bash make_cli.sh

Tensorflow CUDA issues

WIP

Test

https://github.com/google/deepsomatic/blob/r1.9/docs/deepsomatic-case-study-wes.md