install with bioconda

VirMet is available through Bioconda, a channel for the conda package manager. Once conda is installed and the channels are set up, conda install virmet installs the package with all its dependencies.


The classic python install should work, provided the user has the necessary permission. VirMet relies on a number of third-party tools used to access databases, trim, convert, filter and map reads: these are automatically installed if VirMet is installed with conda install. If, for some reason, the user prefers to manually install everything, the tools VirMet depends on are:

  • biopython (Python package)
  • blast >= 2.3
  • bwa
  • entrez-direct (E-utilities from the command line)
  • htslib
  • pandas (Python package)
  • prinseq
  • python (3.x)
  • R with ggplot2 library
  • samtools >= 1.3
  • seqtk

Alternatively, we provide a docker image with everything installed, see instructions for dockerised VirMet.

Commands to install dependencies on Ubuntu

On a Ubuntu 14.04 the following commands should provide a system wide installation of the tools mentioned above (sudo required).

# system wide configuration available as Ubuntu packages
sudo apt-get update -qq
sudo apt-get install -qq -y build-essential ftp golang unzip \
bwa tabix seqtk libwww-perl r-cran-ggplot2

#  NCBI edirect tools
cd /tmp
perl -MNet::FTP -e \
  '$ftp = new Net::FTP("", Passive => 1); $ftp->login;
   $ftp->binary; $ftp->get("/entrez/entrezdirect/");'
unzip -u -q
export PATH=$PATH:/tmp/edirect
cd edirect
sudo install -p econtact edirutil efilter elink entrez-phrase-search eproxy \
espell ftp-cp join-into-groups-of sort-uniq-count-rank xtract xtract.Linux \
eaddress efetch einfo enotify epost esearch esummary ftp-ls nquire \
reorder-columns sort-uniq-count word-at-a-time /usr/local/bin

# prinseq
cd /tmp
wget \
-O /tmp/prinseq-lite-0.20.4.tar.gz
tar -xvf /tmp/prinseq-lite-0.20.4.tar.gz
sudo install -p tmp/prinseq-lite-0.20.4/ /usr/local/bin

# samtools 1.3
wget \
-O /tmp/samtools-1.3.tar.bz2
tar xvfj /tmp/samtools-1.3.tar.bz2
cd /tmp/samtools-1.3
sudo make prefix=/usr/local install

# NCBI blast+ 2.3.0
cd /tmp
tar xzfp ncbi-blast-2.3.0+-x64-linux.tar.gz
sudo install -p ./ncbi-blast-2.3.0+/bin/* /usr/local/bin

# edirect looks for uname in the wrong place
sudo ln -sv /bin/uname /usr/bin/uname

export PATH=/usr/local/bin:$PATH

Then, one needs python 3 (VirMet was mainly developed and tested on 3.4/3.5), but any 3.x should work), together with pandas and Biopython. Go to the respective installation pages and choose your favourite method.