Repository revision
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Repository jbrowse
Name: jbrowse
Owner: iuc
Synopsis: JBrowse Genome Browser integrated as a Galaxy Tool
JBrowse is a fast, extensible JS+HTML5 genome browser.

This repository contains a couple of tools aimed at building up a complete
JBrowse Genome Browser deployment from raw data files such as gff3, bed, bam,
vcf, blastxml, and more...

The tools produce a ready-to-deploy HTML file and associated processed
datasets, allowing visualization of the genome either from within Galaxy, or
outside of Galaxy.

The tool must be whitelisted for HTML content. If BAM files are displayed, it
must be served from an apache or nginx server implementing sendfile.

https://jbrowse.org
Content homepage: https://jbrowse.org
Development repository: https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse
Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/iuc/jbrowse/d022577ff9cf
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/jbrowse
Type: unrestricted
Revision: 4:d022577ff9cf
This revision can be installed: True
Times cloned / installed: 5146
Dependencies of this repository

Repository dependencies - installation of these additional repositories is required
Repository package_perl_5_18 revision 35f117d7396b owned by iuc (prior install required)
Repository package_perl_bundle_jbrowse_1_12_0 revision 52153ec17769 owned by iuc (prior install required)
Repository package_gnu_coreutils_8_25 revision a177f177d42f owned by iuc (prior install required)
Repository package_perl_5_18 revision 35f117d7396b owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_readline_6_3 revision ca1a9400d4e1 owned by iuc (prior install required)
Repository package_bzlib_1_0 revision af4887e1f595 owned by iuc (prior install required)
Repository package_xz_5_0_5 revision 944f93d45594 owned by iuc (prior install required)
Repository package_sqlite_3_8_3 revision c8a5c11cc921 owned by iuc (prior install required)
Repository package_gdbm_1_11 revision ed2537bccffc owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_numpy_1_9 revision 83d12e13dbbd owned by iuc (prior install required)
Repository package_atlas_3_10 revision 98c017ec230d owned by iuc (prior install required)
Repository package_python_2_7 revision f761bd14343e owned by iuc (prior install required)
Repository package_python_2_7_10 revision bd7165ea6526 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_readline_6_3 revision ca1a9400d4e1 owned by iuc (prior install required)
Repository package_bzlib_1_0 revision af4887e1f595 owned by iuc (prior install required)
Repository package_xz_5_0_5 revision 944f93d45594 owned by iuc (prior install required)
Repository package_sqlite_3_8_3 revision c8a5c11cc921 owned by iuc (prior install required)
Repository package_gdbm_1_11 revision ed2537bccffc owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_python_2_7_10 revision bd7165ea6526 owned by iuc (prior install required)
Repository package_libyaml_0_1_5 revision b36f26f0d34b owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_libtool_2_4 revision 7f67694b167c owned by iuc (prior install required)

Tool dependencies - repository tools require handling of these dependencies
Name Version Type
bcbiogff 0.6.2 package
biopython 1.66 package
bundle_jbrowse 1.12.0 package
jbrowse 1.12.0 package
perl 5.18.1 package
python 2.7 package
pyyaml 3.11 package
samtools 1.2 package

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
upgrades the bare data directory to a full JBrowse instance 0.4 any
genome browser 0.4 any

Categories
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
Visualization - Tools for visualizing data