We provide opinionated instructions for installing the external software required by Virtool.
Skewer is used to trim sequencing read data in FASTQ format.
Download the source code
wget https://github.com/relipmoc/skewer/archive/0.2.2.tar.gz
Unpack the archive
tar -xvf 0.2.2.tar.gz
Move into the unpacked directory
cd skewer-0.2.2
Build the skewer binary using make
make
Move the binary to a directory that is in PATH
(eg. /usr/local/bin)
sudo mv skewer /usr/local/bin
Ensure skewer is callable
skewer
You should see the following output:
skewer (0.2.2): No input file specified
Usage: skewer [options] <file> [file2]
Try `skewer --help' for more information.
FastQC is used to calculate quality information from Illumina sample libraries in FASTQ format.
Download the software
wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip
Unpack the archive
unzip fastqc_v0.11.5.zip
Copy the unpacked directory to an installation path such as /opt
sudo cp -rv FastQC /opt
Make the FastQC binary executable
sudo chmod ugo+x /opt/FastQC/fastqc
Make a symbolic link to the binary in a directory in PATH
(eg. /usr/local/bin
)
sudo ln -s /opt/FastQC/fastqc /usr/local/bin/fastqc
Verify that FastQC is callable
fastqc --version
You should see the following output:
FastQC v0.11.5
Bowtie2 is used to map sample reads to references and subtractions.
Download the software.
wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.2/bowtie2-2.3.2-legacy-linux-x86_64.zip
Unpack the archive.
unzip bowtie2-2.3.2-legacy-linux-x86_64.zip
Copy the unpacked directory to an installation path such as /opt
.
sudo cp -rv bowtie2-2.3.2-legacy /opt/bowtie2
Make symbolic links for all binaries in a directory in PATH
(eg. /usr/local/bin
).
sudo ln -s /opt/bowtie2/bowtie* /usr/local/bin
Verify that bowtie2 is callable.
bowtie2 --version
You should see output similar to the following:
/opt/bowtie2/bowtie2-align-s version 2.3.2
64-bit
Built on dde45b53bd81
Sat May 6 02:22:24 UTC 2017
Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-55)
Options: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
Verify that bowtie2-build is callable.
bowtie2-build --version
You should see output similar to the following:
bowtie2-build version 2.3.2
64-bit
Built on dde45b53bd81
Sat May 6 02:22:24 UTC 2017
Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-55)
Options: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
SPAdes is used to assemble sample reads into contigs when detecting novel viral sequences.
Download the software
wget https://github.com/ablab/spades/releases/download/v3.11.1/SPAdes-3.11.1-Linux.tar.gz
Unpack the archive
tar -xvf SPAdes-3.11.1-Linux.tar.gz
Copy the unpacked directory to an installation path such as /opt
sudo cp -rv SPAdes-3.11.1-Linux /opt/spades
Make a symbolic link to the binary in a directory in PATH
(eg. /usr/local/bin
)
sudo ln -s /opt/spades/bin/spades.py /usr/local/bin/spades.py
Verify that spades.py is callable
spades.py --version
You should see an output similar to the following:
SPAdes v3.11.1
HMMER is used to scan for protein motifs in open reading frames (ORF) derived from assembled contigs during novel virus detection.
Download the software
wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz
Unpack the archive
tar -xvf hmmer-3.1b2-linux-intel-x86_64.tar.gz
Copy the unpack directory to an installation path such as /opt
sudo cp -rv hmmer-3.1b2-linux-intel-x86_64 /opt/hmmer
Make symbolic links to all binaries in a directory in PATH
(eg. /usr/local/bin
)
sudo ln -s /opt/hmmer/binaries/* /usr/local/bin
Verify that required HMMER binaries are in PATH
cd ~
hmmscan -h
hmmpress -h
Each command should print an output that begins something like this
# hmmpress :: prepare an HMM database for faster hmmscan searches
# HMMER 3.1b2 (February 2015); http://hmmer.org/
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
FLASH is used to join overlapping Illumina mate pairs in preparation for barcode matching.
Download software
wget http://ccb.jhu.edu/software/FLASH/FLASH-1.2.11-Linux-x86_64.tar.gz
Unpack the software archive
tar -xvf FLASH-1.2.11-Linux-x86_64.tar.gz
Move the binary to a directory that is in PATH
(eg. /usr/local/bin)
mv FLASH-1.2.11-Linux-x86_64/flash /usr/local/bin
Ensure that FLASH is callable
flash --version
You should see the following output:
FLASH v1.2.11
Copyright (C) 2012 Tanja Magoc
Copyright (C) 2012, 2013, 2014 Eric Biggers
License GPLv3+; GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Report bugs to [email protected] or https://sourceforge.net/p/flashpage/bugs
AODP is used to match Illumina amplicon sequencing libraries against barcode target references.
Download software
wget https://bitbucket.org/wenchen_aafc/aodp_v2.0_release/raw/5fcd5d2dfde61cd87ad3c63b8c92babd281fc0dc/aodp-2.5.0.1.tar.gz
Unpack software archive
tar -xvf aodp-2.5.0.1.tar.gz
Move to the unpacked directory
cd aodp-2.5.0.1
Configure build
./configure
Make build
make
Move the binary to a directory that is in PATH
(eg. /usr/local/bin)
mv b/aodp /usr/local/bin/
Ensure that aodp is callable
aodp --version
You should see the following output:
aodp (Automated Oligonucleotide Design Pipeline) 2.5.0.1
(C) HER MAJESTY THE QUEEN IN RIGHT OF CANADA (2014-2018)
(C) Manuel Zahariev [email protected] (2000-2008,2014-2018)
License GPLv3: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
author: Manuel Zahariev, [email protected]