Requirements and Installation¶
Requirements¶
Software¶
- Python 2.7.10+
- Cython 0.25+
- HTSlib
- SAMtools
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | 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
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The following will then need to be on your $PATH:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | 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
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Python Modules¶
- mg-tool-api
- mg-common
- pylint
- pytest
- macs2
Installation¶
Directly from GitHub:
1 | git clone https://github.com/Multiscale-Genomics/mg-process-macs2.git
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Using pip:
1 | pip install git+https://github.com/Multiscale-Genomics/mg-process-macs2.git
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