Requirements and Installation¶
Requirements¶
Software¶
- Python 2.7.10+ or 3.6+
- bedtools (specifically bamtobed)
- bedToBigBed - http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
- wigToBigWig - http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
- BioBamBam2
- Bowtie2
- BWA
- FastQC
- GEMtools
- HDF5
- iNPS
- Kallisto
- libmaus2
- pyenv
- R 2.9.1+
- SAMtools
- MCL
- pigz
Python Modules¶
- numpy
- h5py
- pysam
- pyBigWig
- scipy
- matplotlib
- rpy2
Instructions for the follownig modules are listed in the installation section. All other python modules should be installed with pip prior to the following libraries.
- BS-Seeker2
- TADbit
Installation¶
For a guide to the full installation procedure the Full Installation.
Directly from GitHub:
1 2 3 4 5 | cd ${HOME}/code
git clone https://github.com/Multiscale-Genomics/mg-process-fastq.git
cd mg-process-fastq
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Create the Python environment
1 2 | pyenv-virtualenv 2.7.10 mg-process-fastq
pip install --editable .
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Install the pyTADbit modules
1 2 3 4 5 6 7 | cd ${HOME}/lib
wget https://github.com/3DGenomes/tadbit/archive/master.zip -O tadbit.zip
unzip tadbit.zip
cd tadbit-master
pyenv activate mg-process-fastq
pip install .
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Check out the following software for use by the process_wgbs.py pipeline:
1 2 3 4 5 6 7 8 9 10 11 | cd cd ${HOME}/lib
gti clone https://github.com/BSSeeker/BSseeker2.git
cd ${HOME}/code
cd mg-process-fastq
ln -s $code_root/bs_align bs_align
ln -s $code_root/bs_index bs_index
ln -s $code_root/bs_utils bs_utils
cd cd ${HOME}/code/mg-process-fastq/tool
ln -s $code_root/FilterReads.py FilterReads.py
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Documentation¶
To build the documentation:
1 2 3 4 | pip install Sphinx
pip install sphinx-autobuild
cd docs
make html
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