<commit_before>Requirements and Installation
=============================

`Source (github) <https://github.com/Multiscale-Genomics/mg-process-fastq>`_

Requirements
------------

Software
^^^^^^^^

- bedtools
- 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
- GEMtools
- HDF5
- iNPS
- Kallisto
- libmaus2
- Python 2.7.10+
- pyenv
- R 2.9.1+
- SAMtools
- MCL

Python Modules
^^^^^^^^^^^^^^

- numpy
- h5py
- pysam<commit_msg>Requirement for the bedtools bamtobed script in the WGBS pipeline<commit_after>Requirements and Installation
=============================

`Source (github) <https://github.com/Multiscale-Genomics/mg-process-fastq>`_

Requirements
------------

Software
^^^^^^^^

- 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
- GEMtools
- HDF5
- iNPS
- Kallisto
- libmaus2
- Python 2.7.10+
- pyenv
- R 2.9.1+
- SAMtools
- MCL

Python Modules
^^^^^^^^^^^^^^

- numpy
- h5py
- pysam
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