Setup guide

1. Get the latest version of SwitchSeq

cd installation_dir/
wget -O switchseq-master.zip https://github.com/mgonzalezporta/switchseq/archive/master.zip
unzip switchseq-master.zip

Remember to add SwitchSeq into your PATH by adding the following line into your .bashrc:

export PATH=/path/to/switchseq/:$PATH

2. Run the setup script

SwitchSeq requires both Perl and R to execute, as well as the software listed below. The following command will help you in determining which dependencies are missing, and will install those Perl modules and R packages that are not already present in your system:

cd installation_dir/switchseq-master/
./setup.sh

NOTE: You might need to run the previous script as superuser (sudo), depending on your system configuration. If the execution fails, please proceed to install the required software manually.

Required software

• EMBOSS Needle - more about needle installation
• Perl modules - perl -MCPAN -e "install Module::Name"
  • Getopt::Long
  • Pod::Usage
  • Exporter
  • LWP::Simple
  • List::Util
  • Text::Template
  • JSON
• R Packages
  • tviz - see setup guide

3. Check the installation

Finally, the installation can be checked with the provided tests:

cd installation_dir/switchseq-master/tests
./run_tests.sh

A successful execution will re-generate the directories html_testN, which contain the output for each of the run tests. More details about the specific commands used in the tests and how to interpret the output files can be found in the Tutorial section.