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INSTALL
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ParTIES INSTALLATION
1. SYSTEM REQUIREMENTS
######################
- A UNIX based operating system ( or cygwin unix emulation system for windows ).
- Perl 5.8.0 or higher installed.
2. SOFTWARE REQUIREMENTS
########################
- velvet (1.2.10 or later)
- bowtie2 (2.0.2 or later)
- samtools (0.1.18 or later)
- RepeatMasker (4-0-5 or later)
- blat (v34 or later)
- muscle (3.8.31 or later)
An example install procedure is found at the end of this document.
3. INSTALLATION
###############
- Download the files to the directory you wish to install them in.
git clone https://github.com/oarnaiz/ParTIES
cd ParTIES
- Check the distribution by invoking Perl on the "check" script, i.e.:
perl ./check
The check script will check for you all the pre-requisite software. (See section 4)
- Test ParTIES
perl ./parties
Note : You should see the usage message :
#./parties [MODE] : PARamecium Toolbox for Interspersed DNA Elimination Studies
# Run : Run ParTIES using the configuration file
# Map : Map reads on a reference using bowtie2
# MIRAA : Method of Identification by Read Alignment Anomalies
# MICA : Method of Identification by Comparison of Assemblies
# Insert : Insert IES within a genome to create an IES containing reference
# Assembly : Filter reads and assemble them
# MIRET : Method of Ies RETention
# MILORD : Method of Identification and Localization of Rare Deletion
# Compare : Compare IES/InDel datasets
- Add to your path
Add the following to your $HOME/.bashrc file
export PATH=$PATH:[/path/to/ParTIES]
source $HOME/.bashrc
4. EXAMPLE OF PROCEDURE FOR THE REQUIREMENTS
#############################################
# You need to install zlib-devel (or whatever the equivalent on your server distribution is).
sudo yum install perl-File-Which zlib-devel
# or
sudo apt-get install libfile-which-perl zlib1g-dev
# VELVET
#####################################
mkdir velvet && cd velvet
wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
tar -xzvf velvet_1.2.10.tgz
cd velvet_1.2.10
make 'MAXKMERLENGTH=200' 'LONGSEQUENCES=1' 'OPENMP=1'
# WARNING : When Velvet is installed with 'OPENMP=1' it may generate slightly different assemblies from the same input.
#make install
# BOWTIE2
#####################################
sudo apt-get install bowtie2
# or
mkdir bowtie2 && cd bowtie2
wget http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.0.2/bowtie2-2.0.2-linux-x86_64.zip/download -O bowtie2-2.0.2-linux-x86_64.zip
unzip bowtie2-2.0.2-linux-x86_64.zip
# SAMTools
##########################
sudo apt-get install libncurses5-dev
# or
sudo yum install ncurses ncurses-devel
mkdir samtools && cd samtools
wget http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2/download -O samtools-0.1.18.tar.bz2
bunzip2 samtools-0.1.18.tar.bz2
tar -xvf samtools-0.1.18.tar
cd samtools-0.1.18/
make 'CFLAGS=-g -Wall -O2 -fPIC'
#make install
# RepeatMasker
##########################
# You can skip this step if you do not want to use RepeatMasker (please use -skip_repeat_masker option)
mkdir rmblast && cd rmblast
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/LATEST/ncbi-rmblastn-2.2.28-x64-linux.tar.gz
tar -xzvf ncbi-rmblastn-2.2.28-x64-linux.tar.gz
cd ..
mkdir ncbi-blast && cd ncbi-blast/
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.31+-x64-linux.tar.gz
tar -xzvf ncbi-blast-2.2.31+-x64-linux.tar.gz
cd ncbi-blast-2.2.31+/bin
ln -s ../../../rmblast/ncbi-rmblastn-2.2.28/bin/rmblastn
mkdir trf && cd trf
#go to the URL : https://tandem.bu.edu/trf/trf407b.linux64.download.html
wget http:/...../trf407b.linux64
ln -s trf407b.linux64 trf
mkdir RepeatMasker && cd RepeatMasker
wget http://www.repeatmasker.org/RepeatMasker-open-4-0-5.tar.gz
tar -xzvf RepeatMasker-open-4-0-5.tar.gz
cd RepeatMasker/
./configure
# Update your Repbase libraries on http://www.girinst.org/. (Need an account registration)
# UCSC BLAT
##########################
mkdir blat && cd blat
wget http://genome-test.cse.ucsc.edu/~kent/exe/linux/blatSuite.zip
unzip blatSuite.zip
# MUSCLE
##########################
mkdir muscle && cd muscle
wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
tar -xzvf muscle3.8.31_i86linux64.tar.gz
ln -s muscle3.8.31_i86linux64 muscle
##########################
# PERL MODULES
##########################
su -
cpan
cpan>
cpan> install Statistics::R
cpan> install Parallel::ForkManager
cpan> install Bio::GFF3::LowLevel
cpan> install Bio::DB::Sam
cpan> q