Singularity

Bootstrap: docker
From: ubuntu:18.04

%setup
mkdir -p ${SINGULARITY_ROOTFS}/src/malis
mkdir -p ${SINGULARITY_ROOTFS}/src/mala
mkdir -p ${SINGULARITY_ROOTFS}/src/numcodecs
mkdir -p ${SINGULARITY_ROOTFS}/src/zarr
mkdir -p ${SINGULARITY_ROOTFS}/src/gunpowder
mkdir -p ${SINGULARITY_ROOTFS}/src/daisy
mkdir -p ${SINGULARITY_ROOTFS}/src/synister
mkdir -p ${SINGULARITY_ROOTFS}/src/funlib/learn/torch

%files
synister /src/synister/synister
setup.py /src/synister/setup.py
requirements.txt /src/synister/requirements.txt

%labels
maintainer funkej@janelia.hhmi.org

%post

# basic ubuntu packages

apt update
apt install -y --no-install-recommends \
build-essential \
ca-certificates \
cmake \
git \
libmlpack-dev \
liblzma-dev \
libsm6 \
libxext6 \
libxrender-dev \
libmlpack-dev \
wget && \
rm -rf /var/lib/apt/lists/*

# install conda

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
bash miniconda.sh -b -p /miniconda
PATH="/miniconda/bin:$PATH"
conda config --set always_yes yes --set changeps1 no
conda update -q conda
conda info -a
conda install python=3.6

MALIS_ROOT=/src/malis
MALIS_REPOSITORY=https://github.com/TuragaLab/malis.git
MALIS_REVISION=beb4ee965acee89ab00a20a70205f51177003c69

pip install cython
cd ${MALIS_ROOT}
git clone ${MALIS_REPOSITORY} . && \
git checkout ${MALIS_REVISION}
python setup.py build_ext --inplace
PYTHONPATH=${MALIS_ROOT}:$PYTHONPATH

MALA_ROOT=/src/mala
MALA_REPOSITORY=https://github.com/funkey/mala.git
MALA_REVISION=465b02ffce4204a4c1922f2b316a8b447ec4eb9b

cd ${MALA_ROOT}
git clone ${MALA_REPOSITORY} . && \
git checkout ${MALA_REVISION}
python setup.py build_ext --inplace
PYTHONPATH=${MALA_ROOT}:$PYTHONPATH

NUMCODECS_ROOT=/src/numcodecs
NUMCODECS_REPOSITORY=https://github.com/funkey/numcodecs
NUMCODECS_REVISION=f950047d7b666723f81006cbdfd82c0e6705c39c

cd ${NUMCODECS_ROOT}
git clone ${NUMCODECS_REPOSITORY} . && \
git checkout ${NUMCODECS_REVISION} && \
git submodule update --init --recursive
pip install -r requirements.txt
python setup.py install

ZARR_ROOT=/src/zarr
ZARR_REPOSITORY=https://github.com/funkey/zarr
ZARR_REVISION=9ddf849a6e3329f5ff361ebf6156712926e2fdfe

cd ${ZARR_ROOT}
git clone ${ZARR_REPOSITORY} . && \
git checkout ${ZARR_REVISION}
pip install -r requirements.txt
python setup.py install

GUNPOWDER_ROOT=/src/gunpowder
GUNPOWDER_REPOSITORY=https://github.com/funkey/gunpowder.git
GUNPOWDER_REVISION=754607abcd3c84ec28c0d2ea257b969934ce986d

cd ${GUNPOWDER_ROOT}
git clone ${GUNPOWDER_REPOSITORY} . && \
git checkout ${GUNPOWDER_REVISION}
pip install -r requirements.txt
python setup.py build_ext --inplace
PYTHONPATH=${GUNPOWDER_ROOT}:$PYTHONPATH

DAISY_ROOT=/src/daisy
DAISY_REPOSITORY=https://github.com/funkelab/daisy
DAISY_REVISION=5d0e6c9abbab6a86990d58b3e00ac4332a8ced46

cd ${DAISY_ROOT}
git clone ${DAISY_REPOSITORY} . && \
git checkout ${DAISY_REVISION}
pip install -r requirements.txt
python setup.py build_ext --inplace
PYTHONPATH=${DAISY_ROOT}:$PYTHONPATH

FUNLIB_LEARN_ROOT=/src/funlib/learn/torch
FUNLIB_LEARN_REPOSITORY=https://github.com/funkelab/funlib.learn.torch.git
FUNLIB_LEARN_REVISION=636813e60d48379d078b5458e40bdf23269631b3

cd ${FUNLIB_LEARN_ROOT}
git clone ${FUNLIB_LEARN_REPOSITORY} . && \
git checkout ${FUNLIB_LEARN_REVISION}
#pip install -r requirements.txt
python setup.py build_ext --inplace
PYTHONPATH=${FUNLIB_LEARN_ROOT}:$PYTHONPATH

# install pytorch
conda install pytorch torchvision cudatoolkit=10.2 -c pytorch

# install synister
cd /src/synister
#pip install -r requirements.txt
python setup.py build_ext --inplace
PYTHONPATH=/src/synister:$PYTHONPATH

pip install mahotas
pip install pymongo
pip install opencv-python
pip install iteration_utilities

%environment
export MALIS_ROOT=/src/malis
export PYTHONPATH=${MALIS_ROOT}:$PYTHONPATH
export PYTHONPATH=${AUGMENT_ROOT}:$PYTHONPATH
export PYTHONPATH=${DVISION_ROOT}:$PYTHONPATH
export MALA_ROOT=/src/mala
export PYTHONPATH=${MALA_ROOT}:$PYTHONPATH
export GUNPOWDER_ROOT=/src/gunpowder
export PYTHONPATH=${GUNPOWDER_ROOT}:$PYTHONPATH
export DAISY_ROOT=/src/daisy
export PYTHONPATH=${DAISY_ROOT}:$PYTHONPATH
export PATH=/miniconda/bin:${PATH}
export SYNISTER_ROOT=/src/synister
export PYTHONPATH=${SYNISTER_ROOT}:$PYTHONPATH
export FUNLIB_LEARN_ROOT=/src/funlib/learn/torch
export PYTHONPATH=${FUNLIB_LEARN_ROOT}:$PYTHONPATH

# disable threads for numpy and the like, they get into our way when we
# pre-fetch batches using multiple processes
export OMP_NUM_THREADS=1

%runscript
exec /bin/bash "$@"