Redirected from page "Admin/Tools/Tool Dependencies"

Clear message
Locked History Actions

Admin/Tools/ToolDependencies

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. The version numbers of the tool for the latest version of Galaxy at the last wiki page update is listed here.

If you are maintaining a local or Cloud instance, be certain to check this page regularly when pulling updates from galaxy-central or when pulling from galaxy-dist and alerted of an upgrade in a distribution's Development New Brief.

For how to set up tool dependency directories in your $PATH or Galaxy-specific environment file see: Admin/Config/ToolDependencies

Note that some tool require additional configuration, such as indexes. The application usage notes from the source will note if indexes are needed and how to create them, and the following links will explain how to make the data available to Galaxy with "how-to" guidelines. Data is also available via rsync that mirrors the Galaxy Public Main instance. To learn more about organizing and installing data, such as reference genome builds and indexes, please see: Admin/DataIntegration and Admin/DataPreparation.

Version information is noted in most wrapper's leading source code comments. Inquiries can be sent to: mailto:galaxy-dev@bx.psu.edu

By tool

Section Tool Dependencies (Version)
Lift-Over Convert genome coordinates liftOver (UCSC) ()
Text Manipulation Add column Perl ()
Text Manipulation Cut 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 Group NumPy
Get Genomic Scores Compute phastOdds score NumPy ()
Get Genomic Scores Compute phastOdds score PyTables ()
Fetch Sequences Extract Genomic DNA faToTwoBit ()
Statistics Summary Statistics RPy ()
Statistics Correlation RPy ()
Statistics Compute q-values RPy (),R package 'tcltk' (),R package 'qvalue' ()
Graph/Display Data Histogram RPy ()
Graph/Display Data Scatterplot RPy ()
Graph/Display Data Bar chart NumPy
Graph/Display Data Bar chart Gnuplot (Python) ()
Regional Variation Fetch Indels (3-way) Perl ()
Regional Variation Extract Orthologous Microsatellites sputnik ()
Multiple Alignments ClustalW alignments ClustalW (http://www.clustal.org)
Multiple Regression Perform Linear Regression RPy ()
Multiple Regression Perform Linear Regression NumPy ()
Multiple Regression Perform Best-subsets Regression RPy ()
Multiple Regression Perform Best-subsets Regression NumPy ()
Multiple Regression Perform Best-subsets Regression R package 'leaps' ()
Multiple Regression Compute RCVE RPy ()
Multiple Regression Compute RCVE NumPy ()
Motif Tools Meme Memesuite (http://meme.nbcr.net)
Motif Tools Sequence Logo generator Weblogo3 (http://weblogo.berkeley.edu)
Evolution ALL HYPHY ()
Evolution Neighbor Joining Tree ps2pdf (Ghostscript) ()
Evolution Add scores add_scores (), twoBitToFa (UCSC) ()
Metagenomic analyses Fetch taxonomic representation taxBuilder ()
Metagenomic analyses Summarize taxonomy taxonomy2tree ()
Metagenomic analyses Draw phylogeny taxonomy2tree ()
Metagenomic analyses Draw phylogeny tree2PS-fast ()
Metagenomic analyses Draw phylogeny ps2pdf (Ghostscript) ()
EMBOSS ALL EMBOSS (5.0.0)
NGS: Assembly velveth velvet ()
NGS: Assembly velvetg velvet ()
NGS: QC and manipulation Build base quality distribution RPy ()
NGS: QC and manipulation FastQC from Babraham http://www.bioinformatics.bbsrc.ac.uk FastQC (0.10.0)
NGS: QC and manipulation Fasta Width formatter FastXToolkit
NGS: Picardtools (beta) ALL picardtools (1.76)
NGS: Mapping Map with Bowtie for Illumina bowtie (0.12.7) with bowtie indexes
NGS: Mapping Bowtie2 bowtie2 (2.0.1-2.1.0) with bowtie2 indexes
NGS: Mapping Map with BWA for Illumina BWA (0.5.6)
NGS: Mapping Lastz Lastz (1.01.88)
NGS: Mapping Lastz paired reads Lastz (1.01.88)
NGS: Mapping Map with PerM PerM (0.2.6)
NGS: Mapping Megablast NCBI BLAST+ (BLASTN: Megablast, 2.2.25)
NGS: Mapping Blast+ Blast+ (NCBI BLAST+)
NGS: Mapping Parse megablast xml output cElementTree
NGS: Mapping Map with Bowtie for SOLiD bowtie (0.12.7) with bowtie indexes
NGS: Mapping Map with BWA for SOLiD BWA (0.5.6)
NGS: Peak Calling MACS macs (1.3)
NGS: RNA Analysis Tophat for Illumina tophat (1.3.3-1.4.0) with bowtie + bowtie indexes
NGS: RNA Analysis Tophat2 tophat2 (2.0.9) with bowtie2 + bowtie2 indexes
NGS: RNA Analysis Cufflinks cufflinks (1.3.0-2.1.1)
NGS: RNA Analysis Cuffcompare cufflinks (1.3.0-2.1.1)
NGS: RNA Analysis Cuffmerge cuffmerge (1.3.0-2.1.1)
NGS: RNA Analysis Cuffdiff cuffdiff (2.1.0-2.1.1)
NGS: SAM Tools Filter SAM samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred)
NGS: SAM Tools Convert SAM samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred)
NGS: SAM Tools SAM-to-BAM samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred)
NGS: SAM Tools BAM-to-SAM samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred)
NGS: SAM Tools Merge BAM Files samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred)
NGS: SAM Tools Mpileup samtools (0.1.16-0.1.18), required upgrade
NGS: SAM Tools Generate pileup samtools (0.1.12a-0.1.16, with 0.1.16 strongly preferred), required tool dependency dir config if upgrading other SAM Tools to 0.1.18, see set up help
NGS: SAM Tools Filter pileup samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred)
NGS: SAM Tools Pileup-to-Interval samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred)
NGS: SAM Tools flagstat samtools (0.1.16-0.1.18), required upgrade
NGS: SAM Tools rmdup samtools (0.1.12a-0.1.16, with 0.1.16 strongly preferred)
NGS: GATK Tools (beta) all GATK (1.4)
NGS: Variant Detection FreeBayes FreeBayes (http://github.com/ekg/freebayes); samtools
Human Genome Variation aaChanges Perl (), twoBitToFa (UCSC), cat (), sort ()
Human Genome Variation phyloP add_scores ()
Human Genome Variation SIFT Perl (), bash (), awk (), sed (), rm (), SIFT (JCVI)
Human Genome Variation g:Profiler Perl ()
Human Genome Variation DAVID Perl ()
Human Genome Variation CTD Perl (), LWP::UserAgent (), HTTP::Coolkies ()
Human Genome Variation FunDO Perl ()
Human Genome Variation snpFreq Perl (), R (), R package 'qvalue' ()
Human Genome Variation LD rm ()
Human Genome Variation PASS pass2 (Yu Zhang), sed ()
Human Genome Variation GPASS gpass (Yu Zhang), Perl ()
Human Genome Variation BEAM beam2 (Yu Zhang), Perl (), mv (), rm()
Human Genome Variation LPS lps_tool ()
Human Genome Variation HVIS R (), R package 'HilbertVis' (), awk (), cut (), head ()
Discrete Wavelet Analysis all R (), R packages 'RWave' (), 'wavethresh' (), 'waveslim' ()

By dependency

Dependency (Version) Section Tools
add_scores () Evolution Add scores
Blast+ (NCBI BLAST+) NGS: Mapping Blast+
bowtie (0.12.7) NGS: Mapping Map with Bowtie for Illumina
bowtie (0.12.7) NGS: Mapping Map with Bowtie for SOLiD
bowtie2 (2.0.1-2.1.0) NGS: Mapping Bowtie2
BWA (0.5.6) NGS: Mapping Map with BWA for Illumina
BWA (0.5.6) NGS: Mapping Map with BWA for SOLiD
ClustalW (2.1) Multiple Alignments Align with Clustal
cufflinks (1.3.0-2.1.1) NGS: RNA Analysis Cufflinks
cufflinks (1.3.0-2.1.1) NGS: RNA Analysis Cuffcompare
cuffmerge (1.3.0-2.1.1) NGS: RNA Analysis Cuffmerge
cuffdiff (1.3.0-2.1.1) NGS: RNA Analysis Cuffdiff
cElementTree (Python) () NGS: Mapping Parse megablast xml output
EMBOSS () EMBOSS ALL
FastQC (0.10.0) NGS: QC and manipulation FastQC from Babraham http://www.bioinformatics.bbsrc.ac.uk . Automated administrator installation from the main toolshed is STRONGLY recommended! If you really need to do it manually, the main fastqc perl script must be executable from tool-data/shared/jars/FastQC/fastqc - easiest is to download the tool archive from the Babraham site, unpack it somewhere and move the whole directory to tool-data/shared/jars/FastQC - make sure the fastqc perl script is marked executable by the Galaxy user and that it runs correctly on the command line for the Galaxy user or the tool won't run
GATK (1.4) NGS: GATK Tools (beta) all
FreeBayes (http://github.com/ekg/freebayes); samtools NGS: Variant Detection FreeBayes
Gnuplot (Python) () Graph/Display Data Bar chart
HYPHY () Evolution ALL
R package 'leaps' () Multiple Regression Perform Best-subsets Regression
Lastz (1.01.88) NGS: Mapping Lastz
Lastz (1.01.88) NGS: Mapping Lastz paired reads
liftOver (UCSC) () Lift-Over Convert genome coordinates
macs (1.3) MACS NGS: Peak Calling
NCBI BLAST+ (BLASTN: Megablast, 2.2.25) NGS: Mapping Megablast
NumPy () Graph/Display Data Bar chart
NumPy () Join, Subtract and Group Group
NumPy () Get Genomic Scores Compute phastOdds score
NumPy () Multiple Regression Compute RCVE
NumPy () Multiple Regression Perform Best-subsets Regression
NumPy () Multiple Regression Perform Linear Regression
Perl () Regional Variation Fetch Indels (3-way)
Perl () Text Manipulation Add column
Perl () Text Manipulation Cut
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
PerM (0.2.6) NGS: Mapping Map with PerM
ps2pdf (Ghostscript) () Evolution: HyPhy Neighbor Joining Tree
ps2pdf (Ghostscript) () Metagenomic analyses Draw phylogeny
PyTables () Get Genomic Scores Compute phastOdds score
R package 'leaps' () Multiple Regression Perform Best-subsets Regression
R package 'tcltk' () Statistics Compute q-values
R package 'qvalue' () Statistics Compute q-values
R package 'Rwave' () Discrete Wavelet Analysis all
R package 'wavethresh' () Discrete Wavelet Analysis all
R package 'waveslim' () Discrete Wavelet Analysis all
RPy () Graph/Display Data Histogram
RPy () Graph/Display Data Scatterplot
RPy () Multiple Regression Perform Linear Regression
RPy () Multiple Regression Perform Best-subsets Regression
RPy () Multiple Regression Compute RCVE
RPy () NGS: QC and manipulation Build base quality distribution
RPy () Statistics Correlation
RPy () Statistics Summary Statistics
samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred) NGS: SAM Tools Filter SAM
samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred) NGS: SAM Tools Convert SAM
samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred) NGS: SAM Tools SAM-to-BAM
samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred) NGS: SAM Tools BAM-to-SAM
samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred) NGS: SAM Tools Merge BAM Files
samtools (0.1.16-0.1.18), required upgrade
samtools (0.1.12a-0.1.16, with 0.1.16 strongly preferred), required tool dir config if upgrading other SAM Tools to 0.1.18, see set up help NGS: SAM Tools Generate pileup
samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred) NGS: SAM Tools Filter pileup
samtools (0.1.12-0.1.18 with 0.1.16-0.1.18 strongly preferred) NGS: SAM Tools Pileup-to-Interval
samtools (0.1.16-0.1.18), required upgrade NGS: SAM Tools flagstat
samtools (0.1.12a-0.1.16, with 0.1.16 strongly preferred) NGS: SAM Tools rmdup
sputnik () Regional Variation Extract Orthologous Microsatellites
taxBuilder () Metagenomic analyses Fetch taxonomic representation
taxonomy2tree () Metagenomic analyses Summarize taxonomy
taxonomy2tree () Metagenomic analyses Draw phylogeny
tophat (1.3.3-1.4.0) NGS: RNA Analysis Tophat
tophat2 (2.0.9) NGS: RNA Analysis Tophat2
tree2PS-fast () Metagenomic analyses Draw phylogeny
twoBitToFa (UCSC) () Evolution Add scores
velvet () NGS: Assembly velvetg
velvet () NGS: Assembly velveth
weblogo3 Sequence Logo generator Weblogo3

Sources

Admin/Tools/RGenetics Tool Dependencies for details on SNP/WGA tool dependencies