major problems with plant pipeline

[Turckie]

I have been trying hard but I have to give up. The rice annotation you still provide in the database folder doesn't work in ngsplot.r therefore I tried to run this pipeline but I get error messages all over. Mostly, the *biotype.txt file seems to be the problem. Can you check if it would run through for you?

plant.json

{
"ID":1,
"Assembly": 2,
"Species": 3,
"EnsVer": 4,
"EnsPath": "ftp://ftp.ensemblgenomes.org/pub/release-29/plants/gtf/oryza_sativa/Oryza_sativa.IRGSP-1.0.29.gtf.gz"
}

[shengyinghua]

cause this software used python2，so you need change this #! /usr/bin/env python for python2
#! /usr/bin/env python2
import os
import sys
import string
import re
and I have tired build genome and successfully