The settings for name, version and type from a contained tool configuration file's requirement tag does not match the information for the following tool dependency definitions in the tool_dependencies.xml file, so these tool dependencies have no relationship with any tools within this repository.
* name: bioconductor-edger, type: package, version: 3.14.0
* name: bioconductor-limma, type: package, version: 3.28.10
* name: bowtie, type: package, version: 1.1.2
* name: bowtie2, type: package, version: 2.2.6
* name: deseq2, type: package, version: 1.10.0
* name: eXpress, type: package, version: 1.5.1
* name: rsem, type: package, version: 1.2.28
The settings for name and type from a contained tool configuration file's requirement tag does not match the information for the following tool dependency definitions in the tool_dependencies.xml file, so these tool dependencies have no relationship with any tools within this repository.
* name: TRINITY_MEM_OPTIONS, type: set_environment
Repository revision
Select a revision to inspect and download versions of Galaxy utilities from this repository.

Repository trinity_define_clusters_by_cutting_tree
Name: trinity_define_clusters_by_cutting_tree
Owner: iuc
Synopsis: Partition genes into expression clusters (from the Trinity tool suite)
Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data

https://github.com/trinityrnaseq/trinityrnaseq
Content homepage: https://github.com/trinityrnaseq/trinityrnaseq
Development repository: https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity
Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/iuc/trinity_define_clusters_by_cutting_tree/e4f348d88ae7
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/trinity_define_clusters_by_cutting_tree
Type: unrestricted
Revision: 1:e4f348d88ae7
This revision can be installed: True
Times cloned / installed: 1433
Dependencies of this repository

Repository dependencies - installation of these additional repositories is required
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_lapack_3_4 revision fa453af080f9 owned by iuc (prior install required)
Repository package_bzlib_1_0 revision af4887e1f595 owned by iuc (prior install required)
Repository package_r_3_2_1 revision d9f7d84125b7 owned by iuc (prior install required)
Repository package_atlas_3_10 revision 98c017ec230d owned by iuc (prior install required)
Repository package_readline_6_3 revision ca1a9400d4e1 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 588666932a32 owned by iuc (prior install required)
Repository package_cairo_1_12_14 revision 0a73735c3161 owned by iuc (prior install required)
Repository package_pixman_0_32_6 revision 06f701aa92e2 owned by iuc (prior install required)
Repository package_freetype_2_5_2 revision 1e86d1cf79a4 owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_fontconfig_2_11_1 revision d88d844df0cb owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_r_3_2_1 revision d9f7d84125b7 owned by iuc (prior install required)
Repository package_r_3_2_1 revision d9f7d84125b7 owned by iuc (prior install required)
Repository package_libxml2_2_9_1 revision 45b16a3ab504 owned by iuc (prior install required)
Repository package_cmake_3_2_3 revision 1aea698a1c63 owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 0efde9889efd owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_pixman_0_32_4 revision 32ff063c4de8 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 588666932a32 owned by iuc (prior install required)
Repository package_freetype_2_5_2 revision 1e86d1cf79a4 owned by iuc (prior install required)
Repository package_fontconfig_2_11_1 revision d88d844df0cb owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 588666932a32 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 588666932a32 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 588666932a32 owned by iuc (prior install required)
Repository package_freetype_2_5_2 revision 1e86d1cf79a4 owned by iuc (prior install required)
Repository package_libxml2_2_9_1 revision 45b16a3ab504 owned by iuc (prior install required)
Repository package_bowtie_1_1_2 revision a1c1a92e13a6 owned by iuc
Repository package_bowtie_2_2_6 revision 0d9cd7487cc9 owned by iuc
Repository package_express_1_5_1 revision 93017e8743e5 owned by iuc

Tool dependencies - repository tools require handling of these dependencies
Name Version Type
bioconductor-edger 3.14.0 package
bioconductor-limma 3.28.10 package
bowtie 1.1.2 package
bowtie2 2.2.6 package
deseq2 1.10.0 package
eXpress 1.5.1 package
rsem 1.2.28 package
TRINITY_MEM_OPTIONS set_environment
trinity 2.2.0 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
after differential expression analysis using a Trinity assembly 2.2.0.0 any

Categories
Transcriptomics - Tools for use in the study of Transcriptomics.
RNA - Utilities for RNA