Dependencies

Install dependencies

h1s has some dependencies, that either will be automatically installed via the setup script, or must be installed by your system admin if you don't have the root privileges. In the following you will find the full list of h1s dependencies for Ubuntu system as well as the alternatives for MacOS. In Ubuntu, you can install those system and bioinformatics tools/libraries using apt-get tool

sudo apt-get update -y
sudo apt-get install tool_name -y

In MacOS, we suggest using Homebrew as a replacement for apt-get. After having Homebrew, you can install tools/libraries by using the command

brew install tool_name

In both operation systems, you can install Perl modules using cpanm.

# first, install cpanm
curl -L http://cpanmin.us | perl - --sudo App::cpanminus
# then, install perl module using cpanm
sudo cpanm perl_module_name

If you do not have root privileges, ask your admin to install these dependencies using the setup1s --lib function.

Note: After having all these dependencies installed, you still need to run the setup function setup1s to configure h1s!!!

Dependency list

System tools/libraries

• grep (ggrep)
• sed (gsed)
• wget (wget)
• build-essential
• curl (curl)
• locales
• lib32z1

(In parentheses are Mac's alternative tools)

Bioinformatics tools

• wise (brewsci/bio/genewise)
• hmmer (hmmer)
• ncbi-blast+ (blast)
• blast2
• clustalw (brewsci/bio/clustal-w)
• mafft (mafft)
• muscle (brewsci/bio/muscle)

(In parentheses are Mac's alternative tools)

Perl modules

• Array::Utils
• Capture::Tiny
• DBI
• DB_File
• File::Copy
• File::Path
• File::Basename
• File::Which
• List::Util
• Parallel::ForkManager
• POSIX
• XML::SAX
• XML::NamespaceSupport
• XML::Parser
• Getopt::Long
• IO::Handle
• IPC::Run
• Statistics::R
• Term::Cap
• Time::HiRes
• Bio::AlignIO
• Bio::Align::ProteinStatistics
• Bio::DB::Taxonomy
• Bio::SearchIO
• Bio::SearchIO::blastxml
• Bio::Search::Hit::BlastHit
• Bio::Seq
• Bio::SeqIO
• Bio::SeqUtils
• Bio::Tree::Tree
• Bio::Tools::Run::StandAloneBlast