pyGREAT

https://great-help.atlassian.net/wiki/spaces/GREAT/pages/655447/Programming+Interface

GREAT analysis, http://great.stanford.edu/public/html/, python wrapper

rGREAT is the best if it works for you. But it doesn't work for me.

Motivation

My work here at St. Jude is to develop pipelines and simplify user's effort for NGS analyses. I don't want users, when finish running my HemTools pipeline, have to upload bed files to GREAT server themselves.

Summary

This tool uses Dropbox to create a sharable link and then use it for GREAT analysis. It will print out a GREAT url. You then just need to copypaste the url to a browser to check out the results.

Installation

module load conda3 conda create -n share_url source activate share_url conda install -c anaconda dropbox

Please follow the dropbox instruction below, mainly, you need a token. The dropbox code is taken from: https://gist.github.com/Keshava11/d14db1e22765e8de2670b8976f3c7efb

Usage

python pyGREAT.py test.bed

Return

http://great.stanford.edu/public/cgi-bin/greatStart.php?requestURL=https://www.dropbox.com/s/jd9q2489k91m8bj/test.bed?dl=0&requestSpecies=hg19&requestName=ensGene&requestSender=UCSC%20Table%20Browser