Firstly, we need to setup environments:
source env.shHow to run workflow:
run_toil.sh workflow/rhapsody_wta_1.8/main.cwl data/3DPI-MOCK-2.ymlRestart last workflow without losing any progress:
run_toil.sh -r workflow/rhapsody_wta_1.8/main.cwl data/3DPI-MOCK-2.ymlStart the same workflow from scratch:
run_toil.sh -c workflow/rhapsody_wta_1.8/main.cwl data/3DPI-MOCK-2.ymlRun toil leader within a named screen session:
run_toil.sh -s workflow/rhapsody_wta_1.8/main.cwl data/3DPI-MOCK-2.ymlThe dependencies of LCM-Seq pipeline will be managed by Snakemake, so there's no need to create a conda environment by youself.
source env.sh
run_lcmseq.sh all# Install miniconda
wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh
bash Miniconda3-py39_4.12.0-Linux-x86_64.sh
# Add channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
# Create environments
conda create -n rdev python=3.8
conda activate rdev
conda install -n rdev -c conda-forge r-base=4.2The following dependencies are required for building R packages from sources, you can also install them using system package manager if you have root privilege.
conda install -n rdev -c conda-forge pkg-config gmp libgit2 fftw pandoc hdf5Python package velocyto.py imports numpy and Cython in the file setup.py, so we need to install two of them manually prior to restoring dependencies.
source ./renv/python/virtualenvs/renv-python-3.8/bin/activate
pip install numpy==1.21.6 Cython==0.29.30Restore R packages:
renv::restore()Note: If you have problems compiling packages such as Cairo from sources, you can install r-cairo from conda with the same version to the record in renv.lock. Some of the following packages may require hydration: XML (r-xml), clock (r-clock) and Cairo (r-cairo).
conda install -n rdev -c conda-forge r-cairo=1.6_0Copy the cache from conda using hydrate():
renv::hydrate(packages = "Cairo", sources="~/miniconda3/envs/rdev/lib/R/library")Then continue to renv::restore().