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https://github.com/blahah/transrate-paper
Paper for transrate
https://github.com/blahah/transrate-paper
Last synced: 6 days ago
JSON representation
Paper for transrate
- Host: GitHub
- URL: https://github.com/blahah/transrate-paper
- Owner: blahah
- Created: 2013-11-10T15:12:15.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2016-01-18T12:01:33.000Z (almost 9 years ago)
- Last Synced: 2024-04-16T01:01:04.718Z (7 months ago)
- Language: CSS
- Homepage:
- Size: 75.6 MB
- Stars: 2
- Watchers: 4
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
Transrate: Quality assessment of de-novo transcriptome assemblies
===============
By:
- Richard Smith-Unna (@blahah404)
- Chris Boursnell (@chrisboursnell)
- Rob Patro
- Julian Hibberd
- Steven Kelly
### Description
This is the paper describing transrate (v1). The entire paper is written as a reproducible analysis software package that can be run on a unix system with a single command-line interface.
The paper app will do the following:
- install any software dependencies it needs
- download all the data used in the analysis
- run the analysis pipelines
- generate the figures from the analysis results
### Instructions
#### System requirements
You need:
- a 64 bit unix operating system
- at least 20GB of RAM
- at least 1TB of hard disk space
#### Install
```bash
# get the paper code
$ git clone https://github.com/Blahah/transrate-paper.git
$ cd transrate-paper
# install a fresh ruby...
$ \curl -sSL https://get.rvm.io | bash -s stable --ruby
$ source ~/.rvm/scripts/rvm
# install dependencies
$ bundle install
$ transrate --install-deps all
```
#### Run
Now you can run the paper:
```bash
$ bundle exec bin/transrate-paper --help
```