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install.sh
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install.sh
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#!/bin/bash
## It is an install that assumes a new instance of AWS.
## If you want to install what you need, just select and install.
#==============================base==============================#
sudo apt-get install python
sudo apt-get install make
sudo apt-get update
sudo apt-get install g++
sudo apt-get install c++
#============================== Abyss 2.0 ==============================#
wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.0.2/abyss-2.0.2.tar.gz
tar -xvf abyss-2.0.2.tar.gz
rm abyss-2.0.2.tar.gz
#============================== sparsehash ==============================#
mkdir tool
cd tool
git clone https://github.com/sparsehash/sparsehash.git
cd ./sparsehash
./configure
make
sudo make install
#============================== openMPI ==============================#
cd ~/tool
wget https://www.open-mpi.org/software/ompi/v2.1/downloads/openmpi-2.1.1.tar.gz
tar -xvf openmpi-2.1.1.tar.gz
rm openmpi-2.1.1.tar.gz
cd openmpi-2.1.1
./configure
sudo make install
sudo ldconfig
#============================== Boost ==============================#
cd ~/abyss-2.0.2
wget wget http://downloads.sourceforge.net/project/boost/boost/1.56.0/boost_1_56_0.tar.bz2
tar -xvf boost_1_56_0.tar.bz2
rm boost_1_56_0.tar.bz2
sudo apt-get update
#============================== Abyss 2.0 ==============================#
./configure
make
sudo make install
#============================== Abyss 1 ==============================#
sudo apt-get install abyss
sudo apt-get update
cd ~/tool
# ==============================option_SRAtoolKit ==============================#
wget "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-centos_linux64.tar.gz"
tar -xzf sratoolkit.current-centos_linux64.tar.gz
rm sratoolkit.current-centos_linux64.tar.gz
cd ./sratoolkit.2.8.2-1-centos_linux64/bin
./fastq-dump -I --split-files SRR*****
#./changePairEndFormat.py
mkdir ~/data
mv SRR800798_* ~/data
# you need to change format to use pair-end format.
# check github : https://github.com/cultivo-hy/demo_metassembly/dataFormat/changePairEndFormat.py
# change mode and run ./changePairEndFormat.py. will get pair-end data
cd ~
#============================== SOAPdenovo2 ==============================#
git clone https://github.com/aquaskyline/SOAPdenovo2.git
cd SOAPdenovo2
make
#to run, you make config file " ****.config " see the sample of website or github
# configure file format
# max_rd_len=110
# [LIB]
# avg_ins=200
# asm_flags=3
# reverse_seq=0
# rank=1
# q1=/home/ubuntu/data/SRR800798_1.fastq
# q2=/home/ubuntu/data/SRR800798_2.fastq
#============================== MUMmer ==============================#
sudo apt-get install csh
sudo apt-get install mummer
sudo apt-get update
cd ~
# if the size of your reference sequence is larger than is supported by default,install like this.
# cd ~/tool
# wget https://downloads.sourceforge.net/project/mummer/mummer/3.23/MUMmer3.23.tar.gz
# tar -xvf MUMmer3.23.tar.gz
# cd ./MUMmer3.23
# make check
# cd script
# make
# cd ..
# make CPPFLAGS="-O3 -DSIXTYFOURBITS" << this part make large genome process
# sudo make install
#============================== bowtie2 ==============================#
sudo apt-get install bowtie2
#============================== samtool ==============================#
sudo apt-get install samtools
#============================== argparse ==============================#
sudo apt install python-pip
pip install --upgrade pip
pip install argparse
#==============================[INC] ==============================#
cd ~/tool
wget http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/inc-latest-0.500.tar.gz
tar -xvf inc-latest-0.500.tar.gz
rm inc-latest-0.500.tar.gz
cd inc-latest-0.500
perl Makefile.PL
make
sudo make install
#========================= [Module-build]=========================#
cd ~/tool
wget http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/Module-Build-0.4224.tar.gz
tar -xvf Module-Build-0.4224.tar.gz
rm Module-Build-0.4224.tar.gz
cd Module-Build-0.4224
perl Build.PL
./Build
./Build test
sudo ./Build install
#======================== [List-MoreUtils]========================#
cd ~/tool
wget http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/List-MoreUtils-0.419.tar.gz
tar -xvf List-MoreUtils-0.419.tar.gz
cd List-MoreUtils-0.419
perl Makefile.PL
make
sudo make install
#==================[ Exporter-Tiny-1.000000 ]=====================#
cd ~/tool
wget http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK/Exporter-Tiny-1.000000.tar.gz
tar -xvf Exporter-Tiny-1.000000.tar.gz
rm Exporter-Tiny-1.000000.tar.gz
cd Exporter-Tiny-1.000000
perl Makefile.PL
make
sudo make install
#======================[Statistics-Descript]=======================#
cd ~/tool
wget http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0612.tar.gz
tar -xvf Statistics-Descriptive-3.0612.tar.gz
rm Statistics-Descriptive-3.0612.tar.gz
cd Statistics-Descriptive-3.0612
perl Build.PL
./Build
./Build test
sudo ./Build install
#============================== Metassembly ==============================#
cd ~
wget https://downloads.sourceforge.net/project/metassembler/v1.5/Metassembler.1.5.tar.gz
tar -xvf Metassembler.1.5.tar.gz
rm Metassembler.1.5.tar.gz
cd ~/Metassembler
make
sudo make install
# now run using script. see the sample of website or github