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
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Repository trinity_contig_exn50_statistic
Name: trinity_contig_exn50_statistic
Owner: iuc
Synopsis: Compute contig Ex90N50 statistic and Ex90 transcript count (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_contig_exn50_statistic/1e8a2c87461a
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/trinity_contig_exn50_statistic
Type: unrestricted
Revision: 0:1e8a2c87461a
This revision can be installed: True
Times cloned / installed: 1372

Repository README files - may contain important installation or license information

Readme files
Trinity memory usage ==================== As described on the official Trinity website `FAQ `_, trinity requires a large amount of memory to perform the assembly: "roughly ~1G of RAM per 1M reads to be assembled" By default, this tool is configured to limit the memory consumption to 30G. You might need to lower this limit if the machine(s) executing the jobs have less memory available. If you have a lot of reads to assemble and a machine with enough memory, you can increase it. In both cases, you can edit the TRINITY_MEM_OPTIONS in the file: /environment_settings/TRINITY_MEM_OPTIONS/iuc/trinity//env.sh to lower the maximum memory usage to 2G for example: TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G'
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
from a Trinity assembly 2.2.0.0 any

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