Requirements and Installation

Requirements

Software

  • Python 2.7.10+
  • Cython 0.25+
  • HTSlib
  • SAMtools
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sudo apt-get install make build-essential zlib1g-dev libbz2-dev liblzma-dev curl pigz libncurses5-dev

pip install Cython

cd ${HOME}/lib
git clone https://github.com/samtools/htslib.git
cd htslib
autoheader
autoconf
./configure --prefix=${HOME}/lib/htslib
make
make install

cd ${HOME}/lib
git clone https://github.com/samtools/samtools.git
cd samtools
autoheader
autoconf -Wno-syntax
./configure --prefix=${HOME}/lib/samtools
make
make install

The following will then need to be on your $PATH:

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cd ${HOME}/bin

ln -s ${HOME}/lib/htslib/bin/bgzip bgzip
ln -s ${HOME}/lib/htslib/bin/htsfile htsfile
ln -s ${HOME}/lib/htslib/bin/tabix tabix

ln -s ${HOME}/lib/samtools/bin/ace2sam ace2sam
ln -s ${HOME}/lib/samtools/bin/blast2sam.pl blast2sam.pl
ln -s ${HOME}/lib/samtools/bin/bowtie2sam.pl bowtie2sam.pl
ln -s ${HOME}/lib/samtools/bin/export2sam.pl export2sam.pl
ln -s ${HOME}/lib/samtools/bin/interpolate_sam.pl interpolate_sam.pl
ln -s ${HOME}/lib/samtools/bin/maq2sam-long maq2sam-long
ln -s ${HOME}/lib/samtools/bin/maq2sam-short maq2sam-short
ln -s ${HOME}/lib/samtools/bin/md5fa md5fa
ln -s ${HOME}/lib/samtools/bin/md5sum-lite md5sum-lite
ln -s ${HOME}/lib/samtools/bin/novo2sam.pl novo2sam.pl
ln -s ${HOME}/lib/samtools/bin/plot-bamstats plot-bamstats
ln -s ${HOME}/lib/samtools/bin/psl2sam.pl psl2sam.pl
ln -s ${HOME}/lib/samtools/bin/sam2vcf.pl sam2vcf.pl
ln -s ${HOME}/lib/samtools/bin/samtools samtools
ln -s ${HOME}/lib/samtools/bin/samtools.pl samtools.pl
ln -s ${HOME}/lib/samtools/bin/seq_cache_populate.pl seq_cache_populate.pl
ln -s ${HOME}/lib/samtools/bin/soap2sam.pl soap2sam.pl
ln -s ${HOME}/lib/samtools/bin/varfilter.py varfilter.py
ln -s ${HOME}/lib/samtools/bin/wgsim wgsim
ln -s ${HOME}/lib/samtools/bin/wgsim_eval.pl wgsim_eval.pl
ln -s ${HOME}/lib/samtools/bin/zoom2sam.pl zoom2sam.pl

Python Modules

  • mg-tool-api
  • mg-common
  • pylint
  • pytest
  • macs2

Installation

Directly from GitHub:

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git clone https://github.com/Multiscale-Genomics/mg-process-macs2.git

Using pip:

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pip install git+https://github.com/Multiscale-Genomics/mg-process-macs2.git