Tool Dependencies

Included with Galaxy are all the necessary dependencies to start and run the application framework itself. However the tools themselves may depend on additional applications which are not provided with Galaxy. These dependencies are documented below.

By tool

Section	Tool	Dependencies
Lift-Over	Convert genome coordinates	liftOver (UCSC)
Text Manipulation	Add column	Perl
Text Manipulation	Condense	Perl
Text Manipulation	Convert	Perl
Text Manipulation	Create single interval	Perl
Text Manipulation	Change Case	Perl
Text Manipulation	Paste	Perl
Text Manipulation	Remove beginning	Perl
Text Manipulation	Select first	Perl
Text Manipulation	Select last	Perl
Join, Subtract and Group	Compare two Queries	Perl
Join, Subtract and Group	Group	RPy
Fetch Alignments	MAF Coverage Stats	NumPy
Get Genomic Scores	Compute phastOdds score	NumPy, PyTables
Statistics	Summary Statistics	RPy
Statistics	Correlation	RPy
Graph/Display Data	Histogram	RPy
Graph/Display Data	Scatterplot	RPy
Graph/Display Data	Bar chart	Numeric, Gnuplot (Python)
Graph/Display Data	GMAJ	GMAJ
Graph/Display Data	LAJ	LAJ
Regional Variation	Filter nucleotides	NumPy
Regional Variation	Mask CpG sites	NumPy
Regional Variation	Fetch Indels (pairwise)	NumPy
Regional Variation	Fetch Indels (3-way)	Perl
Regional Variation	Extract Orthologous Microsatellites	sputnik
Evolution: HyPhy	ALL	HYPHY
Evolution: HyPhy	Neighbor Joining Tree	ps2pdf (Ghostscript)
Taxonomy manipulation	Fetch	taxBuilder
Taxonomy manipulation	Summarize	taxonomy2tree
Taxonomy manipulation	Draw	tree2PS-fast
EMBOSS	ALL	EMBOSS
Short Read Analysis	Show Quality Score Distribution	RPy
Short Read Analysis	Histogram	RPy
Short Read Analysis	BLAT	BLAT
Short Read Analysis	Megablast	megablast (NCBI BLAST)
Short Read Analysis	Parse megablast xml output	cElementTree
Short Read Analysis	RMAP	RMAP
Short Read Analysis	RMAPQ	RMAP

By dependency

Dependency	Section	Tools
BLAT	Short Read Analysis	BLAT
cElementTree	Short Read Analysis	Parse megablast xml output
EMBOSS	EMBOSS	ALL
GMAJ	Graph/Display Data	GMAJ
Gnuplot (Python)	Graph/Display Data	Bar chart
HYPHY	Evolution: HyPhy	ALL
LAJ	Graph/Display Data	LAJ
liftOver (UCSC)	Lift-Over	Convert genome coordinates
megablast (NCBI BLAST)	Short Read Analysis	Megablast
Numeric	Graph/Display Data	Bar chart
NumPy	Get Genomic Scores	Compute phastOdds score
NumPy	Fetch Alignments	MAF Coverage Stats
NumPy	Regional Variation	Fetch Indels (pairwise)
NumPy	Regional Variation	Filter nucleotides
NumPy	Regional Variation	Mask CpG sites
Perl	Join, Subtract and Group	Compare two Queries
Perl	Regional Variation	Fetch Indels (3-way)
Perl	Text Manipulation	Add column
Perl	Text Manipulation	Change Case
Perl	Text Manipulation	Condense
Perl	Text Manipulation	Convert
Perl	Text Manipulation	Create single interval
Perl	Text Manipulation	Paste
Perl	Text Manipulation	Remove beginning
Perl	Text Manipulation	Select first
Perl	Text Manipulation	Select last
ps2pdf (Ghostscript)	Evolution: HyPhy	Neighbor Joining Tree
PyTables	Get Genomic Scores	Compute phastOdds score
RPy	Graph/Display Data	Histogram
RPy	Graph/Display Data	Scatterplot
RPy	Join, Subtract and Group	Group
RPy	Short Read Analysis	Histogram
RPy	Short Read Analysis	Show Quality Score Distribution
RPy	Statistics	Correlation
RPy	Statistics	Summary Statistics
RMAP	Short Read Analysis	RMAP
RMAP	Short Read Analysis	RMAPQ
sputnik	Regional Variation	Extract Orthologous Microsatellites
taxBuilder	Taxonomy manipulation	Fetch
taxonomy2tree	Taxonomy manipulation	Summarize
tree2PS-fast	Taxonomy manipulation	Draw

Sources

• BLAT: http://genome.ucsc.edu/FAQ/FAQblat#blat3
• cElementTree: http://effbot.org/zone/celementtree.htm
• EMBOSS: http://emboss.sourceforge.net/
• GMAJ: http://globin.bx.psu.edu/dist/gmaj/
• HYPHY: http://www.hyphy.org/
• LAJ: http://globin.bx.psu.edu/dist/laj/
• liftOver: http://hgdownload.cse.ucsc.edu/admin/exe/
• megablast (NCBI BLAST): http://www.ncbi.nlm.nih.gov/blast/
• Numeric: http://people.csail.mit.edu/jrennie/python/numeric/
• Gnuplot (Python): http://gnuplot-py.sourceforge.net/
• NumPy: http://numpy.scipy.org/
• Perl (ships with almost all operating systems): http://www.perl.com/
• ps2pdf (Ghostscript): http://www.ghostscript.com/
• PyTables: http://www.pytables.org/
• RPy: http://rpy.sourceforge.net/
• RMAP: http://rulai.cshl.edu/rmap/
• sputnik: http://www.bx.psu.edu/svn/universe/dependencies/sputnik/
• taxBuilder, taxonomy2tree, tree2PS-fast: http://dist.g2.bx.psu.edu/

Rgenetics tool dependencies can be found here