Dependencies Updated February 6, 2020

We provide opinionated instructions for installing the external software required by Virtool.

Skewer

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

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

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

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

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

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).
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