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Repository hifive
Name: hifive
Owner: sauria
Synopsis: Contains tools for reading, normalizing, and plotting HiC and 5C chromatin interaction data
HiFive is a set of tools for handling HiC and 5C data. This includes managing data from mapped reads, either in bam, mat, or raw formats. All stages use hdf5 dictionaries for fast access and minimal memory and storage usage.
Content homepage: http://github.com/bxlab/hifive
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/sauria/hifive
Type: unrestricted
Revision: 11:cc95aa05f643
This revision can be installed: True
Times cloned / installed: 148

Repository README files - may contain important installation or license information

Galaxy wrapper for HiFive

This wrapper allows use of the hifive package, a set of tools for handling HiC and 5C data, on Galaxy. This includes managing data from mapped reads, either in bam, mat, or raw formats. All stages use hdf5 dictionaries for fast access and minimal memory and storage usage.

This toolset includes methods for normalizing data from either HiC or 5C experiments at the fragment-end, or fragment level resolution, respectively. Once normalized, data can be used for plotting, binning, or other statistical tests within the package very quickly.

Original documentation can be found here.

Automated Installation

Galaxy should be able to automatically install the dependencies, i.e. the h5py and hifive tool depedency packages.

Manual Installation

For those not using Galaxy's automated installation from the Tool Shed, put the XML and Python files in the tools/hifive/ folder and add the XML files to your tool_conf.xml as normal. For example, use:

<section name="HiFive" id="hifive_tools">
  <tool file="hifive.xml" />
</section>

Wrapper Licence

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Contents of this repository

Name Description Version Minimum Galaxy Version
manipulate, analyze, and plot HiC and 5C chromatin interaction data 0.1.0 16.01

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