pipeone-nm's Introduction

Prerequisites

Docker or conda
Java (version >= 1.7)
Nextflow (version >= 20.07.1.5413)

Installation

1. Download PipeOne-NM

https://github.com/nongbaoting/pipeone-nm.git

2. Setup

2.1 pull docker image or install conda environments

Option 1: pull docker images run by dock

docker push nongbaoting/pipeone_nm:latest

Option 2: install conda environments

bash ./INSTALL/install.sh

2.2 softwares need to be registeration

Trinotate
tmhmm v2 (free academic download) http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm
RNAMMER (free academic download) http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer
signalP v4 (free academic download) http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp

3. Configuration

Modify the program configuration file conf/genomes.config, change the line below:

params {
  genomes {
  "fish_test" {
	refgenome = "/path/to/genome/genomic.fna"
	ref_miRNA = '/path/to/genome/public5/l/FishmiRNA-June2021-dre-mature.fasta'			  // for miranda
	uniprot = "/path/to/genome/uniprot_sprot.pep"                                                     // for Trinotate
	pfam = "/path/to/genome/Pfam-A.hmm"                                                               // for Trinotate
	sqlite = "/path/to/genome/Trinotate_20210616.sqlite"                                         	  // for Trinotate 
	min_length = 150
    }
  }
}

reqiured files which need for Trinotate, you could find this in Trinotate installatio instruction

refgenome
ref_miRNA
uniprot
pfam
sqlite

Run the Pipeline

nextflow run /path/to/pipeOne-nm  -profile docker --sra './sra/*.sra' --genome fish_test

Download RNA-seq data in sra format for test from NCBI
Required Parameters
- RNA-seq data
  - --sra, RNA-seq data in sra format
  - or --fastq, RNA-seq data in fastq format
- --genome, genome version defined in conf/genomes.config,

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