Skip to content

Latest commit

 

History

History
268 lines (202 loc) · 5.23 KB

INSTALL_b38.md

File metadata and controls

268 lines (202 loc) · 5.23 KB

Installation of ClinSV v1.0 from source

We recommend installation from Singularity or Docker images.

This section provides an overview of the dependencies and assistence to compile them from source.

If using local versions of R, Perl or Python is preferred, remove the corresponding symlink in $clinsv_path/bin. Make sure that the required packages are installed.

This installation was tested on CentOS 8

Create a ClinSV installation directory

clinsv_path=$PWD/clinsv
mkdir -p $clinsv_path/bin
export PATH=$clinsv_path/bin:$PATH

Get the latest ClinSV version

  • excluding precompiled dependencies
  1. pre-publication access
wget https://nci.space/clinsv/clinsv_b38/ClinSV_scripts_only_v1.0.tar.gz
tar zxf ClinSV_scripts_only_v1.0.tar.gz
  1. post-publication access
git clone https://github.com/KCCG/ClinSV.git

Install perl and dependencies

Install perl

mkdir $clinsv_path/perl
cd $clinsv_path/perl

wget http://www.cpan.org/src/5.0/perl-5.24.1.tar.gz
tar -xzf perl-5.24.1.tar.gz
cd perl-5.24.1
./Configure -des -Dprefix=$clinsv_path/perl -Duserelocatableinc
make
make test
make install

cd $clinsv_path/perl
rm -r perl-5.24.1*

Install cpanm

cd $clinsv_path/perl
curl -L https://cpanmin.us/ -o cpanm
chmod +x cpanm

create links to bin

cd $clinsv_path/bin
ln -s ../perl/bin/perl perl
ln -s ../perl/cpanm cpanm

Install required perl modules with cpanm

#cpanm Bio::Perl
cpanm Compress::Zlib
cpanm Sort::Naturally
cpanm List::BinarySearch::XS
cpanm Excel::Writer::XLSX
cpanm LWP

Install Tabix perl module

cd $clinsv_path/perl
git clone https://github.com/MinocheAE/tabix.git
cd tabix
make
cd perl
perl Makefile.PL
make
make test
make install

Install Bio::DB::Big perl module

cd $clinsv_path/perl
git clone https://github.com/dpryan79/libBigWig
cd libBigWig/
make
export LIBBIGWIG_DIR=$PWD
cpanm install Bio::DB::Big

Install Samtools BCFtools Tabix BGZip

cd $clinsv_path
mkdir samtools
cd samtools
wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2
wget https://github.com/samtools/bcftools/releases/download/1.10.2/bcftools-1.10.2.tar.bz2
wget https://github.com/samtools/htslib/releases/download/1.10.2/htslib-1.10.2.tar.bz2

tar xvfj samtools-1.10.tar.bz2
tar xvfj bcftools-1.10.2.tar.bz2
tar xvfj htslib-1.10.2.tar.bz2

cd htslib*
make; make prefix=$clinsv_path/samtools install

cd ../samtools*
make; make prefix=$clinsv_path/samtools install

cd ../bcftools*
make; make prefix=$clinsv_path/samtools install

cd ..
rm -r htslib* samtools* bcftools*

cd $clinsv_path/bin
ln -s ../samtools/bin/bcftools bcftools
ln -s ../samtools/bin/samtools samtools
ln -s ../samtools/bin/bgzip bgzip
ln -s ../samtools/bin/tabix tabix

Install BigWigTools

For source and binaries please refer to: http://hgdownload.soe.ucsc.edu/admin/exe/

Save the binaries into: $clinsv_path/bigWigTools

mkdir $clinsv_path/bigWigTools
cd $clinsv_path/bigWigTools
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/bigWigToWig
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/wigToBigWig
chmod ug+x $clinsv_path/bigWigTools/*

cd $clinsv_path/bin
ln -s ../bigWigTools/bigWigToWig bigWigToWig
ln -s ../bigWigTools/wigToBigWig wigToBigWig

Install Python

mkdir $clinsv_path/python
cd $clinsv_path/python

wget https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tgz
tar zxf Python-2.7.18.tgz
cd Python-2.7.18
./configure  --prefix=$clinsv_path/python
make
make install

cd $clinsv_path/python
rm -r Python-2.7.18*

curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
./bin/python get-pip.py

cd $clinsv_path/bin
ln -s ../python/bin/python python
ln -s ../python/bin/python python2
ln -s ../python/bin/pip pip

install python modules

pip install numpy
pip install pysam

Install CNVnator

For installing CNVnator https://github.com/hall-lab/speedseq#installation

Install root

Compilling root rarely works on the first attempt. As long as CNVnator runs without error messages a partial compillation is sufficient.

cd $clinsv_path

wget https://root.cern.ch/download/root_v5.34.38.source.tar.gz
tar -zxf root_v5.34.38.source.tar.gz
cd root
./configure
make

source $PWD/bin/thisroot.sh

Install CNVnator-multi

mkdir $clinsv_path/cnvnator-multi
cd $clinsv_path/cnvnator-multi

git clone --recursive https://github.com/hall-lab/speedseq
cd speedseq
make cnvnator
  • The -std=c++11 may need to be removed from src/CNVnator/Makefile
cd $clinsv_path/cnvnator-multi
ln -s speedseq/bin/cnvnator cnvnator-multi .
ln -s speedseq/bin/cnvnator_wrapper.py .

Install Lumpy

cd $clinsv_path
git clone --recursive https://github.com/arq5x/lumpy-sv.git
cd lumpy-sv
make

cd $clinsv_path/bin
ln -s ../lumpy-sv/bin/lumpy lumpy

Install R

mkdir $clinsv_path/R
cd $clinsv_path/R
wget http://cran.rstudio.com/src/base/R-3/R-3.2.3.tar.gz
tar zxf R-3.2.3.tar.gz
cd R-3.2.3
./configure --prefix=$clinsv_path/R
make
make install

cd $clinsv_path/bin
ln -s ../R/bin/R R

rm -fr $clinsv_path/R/R-3.2.3*

install R package knitr locally

cd $clinsv_path/R/lib64/R/library
R
.libPaths(getwd())
install.packages("knitr", getwd(),repos='http://cran.rstudio.org');
library("knitr");
quit(save="no")