VADR Install Guide for Biolinux

1. Clone the Repo

First, make sure that you are inside of the root directory of the tostadas repository, and then run the following:

git clone https://github.com/ncbi/vadr.git
cd vadr
VADRINSTALLDIR=$PWD

2. Run the Install Script, If Getting an Error with Curl, Install Curl Using Mamba

mamba install -c conda-forge curl

Windows:

bash vadr-install.sh linux

Mac:

bash vadr-install.sh macosx

Troubleshooting:

If you receive the following error message:

vadr-install.sh: line 174: autoconf: command not found

Then, install autoconf using either of the following commands:

sudo apt-get install autoconf

OR

brew install autoconf

3. Set Up the MPXV Model Directory

curl https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/mpxv/1.4.2-1/vadr-models-mpxv-1.4.2-1.tar.gz --output mpxv-models.tar.gz
tar -xf mpxv-models.tar.gz && mv vadr-models-mpxv-* mpxv-models

You also need to copy the modified model file that includes the ITRs from our MPXV repo. cp ../vadr_files/mpxv.rpt.minfo mpxv-models/

4. Export PATHS

Or add to your .bashrc profile

Use env_variables.sh file to export path variables:

cd .. && . vadr_files/env_variables.sh

5. Test and Troubleshoot the Install

Test your install by running perl vadr/v-annotate.pl.

It will probably fail with either (1) use: command not found or (2) Cant locate XYZ package in @INC.

If it works as expected, skip to #5 to export your variables. Else, you can now begin the process of troubleshooting by installing the required PERL libraries.

To Install Bio/Easel/MSA.pl

perl vadr/Bio-Easel/Makefile.PL
cd vadr/Bio-Easel
make
make install

** If make install throws a permission error, try running it as admin with sudo make install instead

To Install LWP/Simple.pm

cpan install LWP

If error about sqp_opts.pm copy the files in sequip to your Perl path, which is shown as the @INC cp sequip/* <YOUR_PATH>

6. Run the annotation script

Ideally you have as many threads as samples, since VADR will give one thread to each sample

perl vadr/v-annotate.pl --split --cpu 8 --glsearch --minimap2 -s -r --nomisc \
--r_lowsimok --r_lowsimxd 100 --r_lowsimxl 2000 --alt_pass \
discontn,dupregin --s_overhang 150 -i vadr/mpxv-models/mpxv.rpt.minfo -n \
vadr/mpxv-models/mpxv.fa -x $MDIR input_files/trialDatav5.fasta \
vadr_testing_outdir -f

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Last update: 2025-03-26