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Installation

Quick installation

mkdir ~/bin
cd bin
git clone https://github.com/lskatz/SneakerNet.git
cd SneakerNet

# the following two lines are for local installations
cpanm --local-lib=$HOME local::lib && eval $(perl -I $HOME/lib/perl5/ -Mlocal::lib)
export PERL5LIB=$PERL5LIB:$HOME/lib/perl5:$HOME/lib/perl5/x86_64-linux-gnu-thread-multi:$HOME/lib/perl5/x86_64-linux-gnu-thread-multi/auto

# The following lines are regardless of local or global installation
cpanm version::vpp
cpanm --installdeps --notest . -l .
perl Makefile.PL
make

Test the installation

make test

Dependencies

Resources

The minimum requirements are about 4G RAM, but 8G RAM is recommended. An average run with only 1 thread is about 200 minutes; however with 4 threads, the run time gets down to about 9 minutes. For more information: #42 (comment)

Software

There are few core dependencies. However, SneakerNet is based on plugins that have individual dependencies. Here is a list of dependencies across the board, although it is possible that all of the following are not needed for a complete SneakerNet analysis.

To find the right dependencies for you, run the following

SneakerNet.checkdeps.pl --list  # and find the workflow, e.g., 'default'
SneakerNet.checkdeps.pl default # Check deps for all plugins for the workflow 'default'

Comprehensive list

This list was created using SneakerNet.checkdeps.pl [iontorrent metagenomics cryptosporidium default] on version 0.8.14. Dependencies may or may not have changed since then but they can still be checked using this script.

All workflows require perl v5.12 or higher, compiled with multithreading. This version of perl is already installed in most modern Linux operating systems.

Default workflow
metagenomics
cryptosporidium
iontorrent
Non-workflow
SneakerNet.roRun.pl
  • bcl2fastq

Configuration

You will need to edit some files for configuration before using SneakerNet.

$ cp -r config.bak config
$ cd config

Some settings are necessary to change in the config/*.conf files. Please edit these files accordingly.

Special variables are allowed and have a VAR format. These are the variables currently allowed

  • __BASE__ evaluates to the installation directory of SneakerNet. Useful for file paths, e.g., location of where a bed file is.

emails

List any emails here, comma-separated. These emails will be sent reports by default for each SneakerNet run.

taxonProperties

see INSTALL.taxonProperties.md for more information

Each taxon that you might have sequences for is defined here. If not defined here, nothing bad will happen though. For each taxon, you can show the minimum quality and coverage thresholds; the genome size in bp; the regular expression to match filename to taxon; and the destination folder on the remote computer.

settings

This file has certain key/values and should be carefully edited. Some individual plugin settings are found here.

plugins

This file defines workflows. The first keyword is the workflow. After the equals sign, a number of plugins are listed and delimited by commas. They are shown in order of execution. For example, all assembly-based plugins must appear after the genome assembly plugin runs.

You are able to create your own workflow or use the pre-defined ones here.

Each workflow is listed in the SneakerNet snok.txt file in the format of workflow = default where in this example the default workflow is invoked. If no workflow is given in snok.txt or if snok.txt is missing, the default workflow will be used.