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Requirements

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Nick Youngblut edited this page Jun 4, 2014 · 9 revisions

These are the software requirements for running various workflows of CLdb. Not all are needed for all workflows.

Perl modules

These should all be easy to install with CPAN or cpan-minus

BioPerl (tested on v1.006901)
Set::IntervalTree
Parallel::ForkManager
Regexp::Common
IPC::Cmd
List::MoreUtils
Sereal

Database construction

sqlite3 (tested on v3.7.17)

Spacer, direct repeat, and leader clustering

cd-hit-est (tested on v4.6)

Alignments of leader regions

mafft (tested on v7.037b)

Spacer blasting

blast+ toolkit (tested on 2.2.27+)

Plotting loci

R (tested on v3.0.1)
R package: genoPlotR (tested on v0.8)
ITEP (if coloring genes by gene cluster in loci plots)