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cistrome-to-multivec

README.md

pipelines/cistrome-to-multivec

Generate multivec files from CistromeDB bigWig files.

conda activate cistrome-to-multivec-pipeline
# to generate multivec outputs
snakemake --cores 2 --config filetype=mv5
# or, to generate zarr outputs
snakemake --cores 2 --config filetype=zarr
# or, if on O2 (replace with your O2 username)
./submit.sh mv5 my_username

Setup

Create conda environment

conda env create -f environment.yml
conda activate cistrome-to-multivec-pipeline

Copy snakemake cluster config

mkdir -p ~/.config/snakemake/cistrome-explorer
cp ./cluster-profile.yml ~/.config/snakemake/cistrome-explorer/config.yaml

Sync output files with s3 bucket

# replace with your credentials
export AWS_ACCESS_KEY_ID="{my_access_key_id}"
export AWS_SECRET_ACCESS_KEY="{my_secret_access_key}"
export AWS_DEFAULT_REGION="us-east-1"

# replace with your O2 username details
# .../users/{first_letter_of_username}/{username}/cistrome-explorer/...
aws s3 sync /n/scratch3/users/m/mk596/cistrome-explorer/data/processed/ s3://higlass-server/CistromeDB/

Using parallel hdf5 via h5py and mpi4py

The following info is outdated, since h5py does not yet work with the parallel version of hdf5 installed on the o2 cluster. In the meantime we can do parallelization by submitting many simultaneous snakemake jobs for each output bigwig file.

https://docs.h5py.org/en/latest/build.html#building-against-parallel-hdf5

On O2

module load gcc/6.2.0
module load openmpi/3.1.0
module load hdf5/1.12.0

which mpicc
which h5cc # doesn't work for some reason - but the hdf5 dir is /n/app/hdf5/1.12.0.parallel

# CC="mpicc" HDF5_MPI="ON" HDF5_DIR=/n/app/hdf5/1.12.0.parallel pip install --no-binary=h5py h5py # doesn't work since pip h5py not compatible with 1.12.0

cd path/to/h5py-parent
# Clone h5py so that the latest code with support for hdf5 v1.12.0 (since not yet on pip).
git clone git@github.com:h5py/h5py.git

cd h5py
python setup.py configure --hdf5=/n/app/hdf5/1.12.0.parallel
python setup.py configure --mpi
python setup.py install

On macOS

Download hdf5 1.10.6 source code from https://www.hdfgroup.org/downloads/hdf5/source-code/ and un-tar-gz

brew install openmpi

# Make a directory in which hdf5 can be installed.
mkdir -p ~/software/hdf5

brew info openmpi # Use this to find the CC value for the next line.

# In the downloaded hdf5-1.10.6 source directory:
CC=/usr/local/Cellar/open-mpi/4.0.3/bin/mpicc ./configure --enable-parallel --enable-shared --prefix=$HOME/software/hdf5
make
export NPROCS=3 # https://github.com/open-mpi/ompi/issues/6497
make check
make install

cd path/to/h5py-parent
# Clone h5py so that the latest code with support for hdf5 v1.12.0 (since not yet on pip).
git clone git@github.com:h5py/h5py.git

cd h5py
export CC=/usr/local/Cellar/open-mpi/4.0.3/bin/mpicc
python setup.py configure --hdf5=$HOME/software/hdf5
python setup.py configure --mpi
python setup.py install
cd ..
python
>>> import h5py
>>> h5py.get_config().mpi # Should return True if MPI has been enabled