galaxy / galaxy-central
Main development repository for Galaxy. Active development happens here, and this repository is thus intended for those working on Galaxy development. See http://bitbucket.org/galaxy/galaxy-dist/ for a more stable repository intended for end-users.
Clone this repository (size: 44.8 MB): HTTPS / SSH
$ hg clone http://bitbucket.org/galaxy/galaxy-central/
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) | ||||
| 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 | RMAP | RMAP | ||||
| Short Read Analysis | RMAPQ | RMAP | ||||
| NGS: QC and manipulation | FASTQ Groomer | fq_all2std.pl (MAQ) | ||||
| NGS: Mapping | Megablast | megablast (NCBI BLAST) | ||||
| NGS: Mapping | Parse megablast xml output | cElementTree | ||||
| NGS: Mapping | Map with Bowtie | bowtie | ||||
| NGS: Mapping | Map with BWA | BWA | ||||
| NGS: SAM Tools | SAM-to-BAM | samtools | ||||
| NGS: SAM Tools | Merge BAM Files | samtools | ||||
| NGS: SAM Tools | Generate pileup | samtools |
By dependency
| Dependency | Section | Tools | ||||
| BLAT | Short Read Analysis | BLAT | ||||
| bowtie | NGS: Mapping | Map with Bowtie | ||||
| BWA | NGS: Mapping | Map with BWA | ||||
| cElementTree | NGS: Mapping | Parse megablast xml output | ||||
| EMBOSS | EMBOSS | ALL | ||||
| fq_all2std.pl (MAQ) | NGS: QC manipulation | FASTQ Groomer | ||||
| Gnuplot (Python) | Graph/Display Data | Bar chart | ||||
| HYPHY | Evolution: !HyPhy | ALL | ||||
| liftOver (UCSC) | Lift-Over | Convert genome coordinates | ||||
| megablast (NCBI BLAST) | NGS: Mapping | 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 | ||||
| samtools | NGS: SAM Tools | SAM-to-BAM | ||||
| samtools | NGS: SAM Tools | Merge BAM Files | ||||
| samtools | NGS: SAM Tools | Generate pileup | ||||
| 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/
- bowtie: http://bowtie-bio.sourceforge.net/index.shtml
- BWA: http://bio-bwa.sourceforge.net/
- samtools: http://samtools.sourceforge.net/
- MAQ: http://maq.sourceforge.net/
Rgenetics tool dependencies can be found here
This revision is from 2009-11-18 18:15