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Repository s_mart
Name: s_mart
Owner: yufei-luo
Synopsis: S-MART manages your RNA-Seq and ChIP-Seq data. It also produces many different plots to visualize your data.
 Several tools are now available for mapping high-throughput sequencing data from a genome, but few can extract biological knowledge from the mapped reads. We have developed a toolbox, S-MART, which handles mapped RNA-Seq and ChIP-Seq data. S-MART is created by Matthias Zytnicki (URGI, INRA Versailles, France).
S-MART is an intuitive and lightweight tool, performing several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization.

It includes the selection (or the exclusion) of the data that overlaps with a reference set, clustering and comparative analysis (between two conditions, for instance). S-MART also provides many ways to visualize your data: size of the reads, density on the genome, distance with respect to a reference set, and the correlation of two data sets (with cloud plots).
S-MART does not require a computer science background and thus can be used by all biologists through a graphical interface. S-MART can run on any personal computer, yielding results within an hour for most queries. S-MART manages your RNA-Seq and ChIP-Seq data. It also produces many different plots to visualize your data.
Type: unrestricted
Revision: 71:d96f6c9a39e0
This revision can be installed: True
Times cloned / installed: 3277

Repository README files - may contain important installation or license information

|  NAME  |

Several tools are now available for mapping high-throughput sequencing data from a genome, but few can extract biological knowledge from the mapped reads. We have developed a toolbox, S-MART, which handles mapped RNA-Seq and ChIP-Seq data.

S-MART is an intuitive and lightweight tool, performing several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization.

S-MART does not require a computer science background and thus can be used by all biologists through a graphical interface. S-MART can run on any personal computer, yielding results within an hour for most queries. 

Copyright INRA-URGI 2009-2013

Matthias Zytnicki


This library is distributed under the terms of the CeCILL license 
See the LICENSE.txt file.

Installation under Galaxy
S-MART is available under the Galaxy Tool Shed:
Remember to set the variables "tool_config_file" and "tool_dependency_dir" accordingly. Please look up the Galaxy Tool Shed wiki to know more about it.
It assumes you have R installed, as well as two packages: RColorBrewer (for colors in graphics), and Hmisc (for statistics). You can install them as root with the commands:
 - R --slave --no-save --no-restore --quiet -e 'if("RColorBrewer" %in% rownames(installed.packages()) == FALSE){install.packages("RColorBrewer", repos = c(""), dependencies = TRUE)}'
 - R --slave --no-save --no-restore --quiet -e 'if("Hmisc" %in% rownames(installed.packages()) == FALSE){install.packages("Hmisc", repos = c(""), dependencies = TRUE)}'

Optionally, you can organize the layout of S-MART tools following these instructions. This way, all the tools will be correctly sorted and appear in categories.
 - Locate the directory where S-MART has been installed: probably in "<galaxy install dir>/shed_tool/"
 - Create a symbolic link "<galaxy install dir>/tools/s_mart" directing to "<S-MART install dir>/SMART/galaxy/"
 - Paste the content of "<S-MART install dir>/SMART/galaxy/tool_conf.xml" to your local "<galaxy install dir>/tool_conf.xml", for instance, right before the </toolbox> mark-up.
 - Remove the S-MART layout in "<galaxy install dir>/shed_tool_conf.xml" (the name may vary depending on your "universe_wgsi.ini" file) which has been automatically generated: remove the whole block between the markup <section id="s-mart" name="S-MART" version="XXX"> and the corresponding </section>.
 - Restart Galaxy to complete the install.

Stand-alone installation
This product needs the following softwares :
 - R, under the GNU General Public License, and several R package (under the same License)
 - Python, under the Python License, compatible with the GNU General Public License
 - Java, under the GNU General Public License

Further installation instructions and the user guide are available in the file "doc.pdf".

Many thanks go helping developers:
 - Yufei Luo
 - the URGI team
and the beta-testers:
 - Claire Toffano-Nioche
 - Claire Kuchly
 - among others...
Dependencies of this repository

Name Version Type
PYTHONPATH set_environment

Contents of this repository

Name Description Version Minimum Galaxy Version
Convert a file from a format to another. 1.0.0 any
Select the features which are located in a given locus. 1.0.0 any
Provide the queries that overlap with a reference, when the query data set is small. 1.0.0 any
Get the introns of a set of transcripts. 1.0.0 any
Compute the average data around some genomic coordinates using WIG files (thus covering a large proportion of the genome). 1.0.0 any
Get the differential expression between 2 conditions using Fisher's exact test, on regions defined by a third file. 1.0.0 any
Select the elements of a list of sequences or transcripts with a given size. 1.0.0 any
Extend or shring a list of sequences. 1.0.0 any
Get the flanking regions of a set of reference. 1.0.0 any
Merges two genomic features if they have exactly the same genomic coordinates. 1.0.0 any
Give the distances between every data from the first input set with respect to the data from the second input set. 1.0.0 any
Get the sizes of a set of genomic coordinates. 1.0.0 any
Merges two files containing the results of a sliding windows clustering. 1.0.0 any
Extend or shrink a list of genomic coordinates. 1.0.0 any
Get the exons of a set of transcripts. 1.0.0 any
Get Distribution: Get the distribution of the genomic coordinates along a genome. 1.0.0 any
Removes the introns of the transcript files. 1.0.0 any
Clusterize features when their genomic intervals overlap. 1.0.0 any
Gets all the regions of the genome, except the one given in an annotation file. Alternatively, it may also give all the elements from the first set which does not ovelap with the second set (at the nucleotide level). 1.0.0 any
Provide the queries that overlap with a reference, when the query data set is small. 1.0.0 any
Produces a GFF3 file that clusters a list of transcripts using a sliding window. Cluster the data into regions (defined by size and overlap with next region). 1.0.0 any
Remove the 5' and/or 3' adapters of a list of reads. 1.0.0 any
Calculate distribution for each nucleotide per position for all short reads 1.0.0 any
Change a feature in a GFF file (the feature is the 3rd column). 1.0.0 any
Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome). 1.0.0 any
Change the name of a tag in a GFF file. 1.0.0 any
Plot the coverage of the first data with respect to the second one. 1.0.0 any
Merge the elements of two lists of genomic coordinates. 1.0.0 any
Compute the coverage of a set with respect to another set. 1.0.0 any
Keep the genomic coordinates such that a value of a given tag. 1.0.0 any
Compute the average data for some genomic coordinates using WIG files 1.0.0 any
Get Read Distribution v1.0.1: Plot the number of identical reads and give the most represented. 1.0.0 any
Plot some information from a list of transcripts. 1.0.0 any
Count GC percent for each read against a genome. 1.0.0 any
Clean a transcript file so that it is useable for S-MART. 1.0.0 any
Removes the introns of the transcript files. 1.0.0 any
Coordinates to Sequences: Extract the sequences from a list of coordinates. 1.0.0 any
Provide the queries that overlap with a reference. 1.0.0 any
Read the output of an aligner, print statistics and possibly translate into GFF, BED or GBrowse formats. 1.0.0 any

Convert Formats - Tools for converting data formats
Fasta Manipulation - Tools for manipulating fasta data
Genomic Interval Operations - Tools for operating on genomic intervals
Next Gen Mappers - Tools for the analysis and handling of Next Gen sequencing data
SAM - Tools for manipulating alignments in the SAM format
Visualization - Tools for visualizing data