Galaxy Wiki
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/Tool Dependencies
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/Data Integration and Admin/NGS Local Setup.
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 | RPy (), R package 'prettyR' (), 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 | 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 (2.0.1-2.0.4) 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 (2.0.6) 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 (2.0.1-2.0.4) | 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. The main fastqc perl script must be executable from tool-data/shared/jars/FastQC/fastqc |
| 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 'prettyR' () | Join, Subtract and Group | Group |
| 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 () | Join, Subtract and Group | Group |
| 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 (2.0.6) | 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
- add_scores: http://bitbucket.org/natefoo/add_scores
- beam2: http://stat.psu.edu/~yuzhang/software/beam2_source.tar
- blast+ (NCBI BLAST+): http://blast.ncbi.nlm.nih.gov/Blast.cgi
- bowtie: http://bowtie-bio.sourceforge.net/index.shtml
- bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
- BWA: http://bio-bwa.sourceforge.net/
- cElementTree: http://effbot.org/zone/celementtree.htm
- clustalw: http://www.clustal.org
- cufflinks, cuffcompare, cuffmerge, cuffdiff & gtf_to_sam: http://cufflinks.cbcb.umd.edu/
- EMBOSS: http://emboss.sourceforge.net/
- FastQC: http://www.bioinformatics.bbsrc.ac.uk/
- FastXToolkit: http://hannonlab.cshl.edu/fastx_toolkit/
- FreeBayes: http://bioinformatics.bc.edu/marthlab/FreeBayes/
- GATK: http://www.broadinstitute.org/gsa/wiki/
- GMAJ: http://globin.bx.psu.edu/dist/gmaj/
- Gnuplot (Python): http://gnuplot-py.sourceforge.net/
- gpass: http://stat.psu.edu/~yuzhang/software/<<nwwl(GPASS)>>.tar
- HYPHY: http://www.hyphy.org/
- LAJ: http://globin.bx.psu.edu/dist/laj/
- lastz: http://www.bx.psu.edu/miller_lab/dist/
- liftOver, twoBitToFa, faToTwoBit: http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/utils/ (source), http://hgdownload.cse.ucsc.edu/admin/exe/ (binaries)
- lps_tool: http://www.bx.psu.edu/miller_lab/dist/lps_tool.latest.tar.gz
- pass2: http://stat.psu.edu/~yuzhang/software/pass2_source.tar
- R package 'leaps': http://cran.r-project.org/web/packages/leaps/
- macs: http://liulab.dfci.harvard.edu/MACS/
- NumPy: http://numpy.scipy.org/
- Perl (ships with almost all operating systems): http://www.perl.com/
- PerM: http://code.google.com/p/perm/
- ps2pdf, Ghostscript: http://www.ghostscript.com/
- PyTables: http://www.pytables.org/
- R: http://www.r-project.org/
- RPy: http://rpy.sourceforge.net/
- samtools: http://samtools.sourceforge.net/
- SIFT: http://sift.jcvi.org/
- sputnik: http://bitbucket.org/natefoo/sputnik-mononucleotide/
- taxBuilder, taxonomy2tree, tree2PS-fast: http://bitbucket.org/natefoo/taxonomy
- tophat/tophat2: http://tophat.cbcb.umd.edu/index.html
- velvet: http://www.ebi.ac.uk/~zerbino/velvet/
- weblogo3: http://weblogo.threeplusone.com/
Admin/Tools/RGenetics Tool Dependencies for details on SNP/WGA tool dependencies