rainbowRNA

RNAseq网页自动化流程

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报告预览

Installation

1. If conda is not installed in /home/"user"/miniconda3, download and install miniconda, and configure the miniconda environment.
   

wget -c https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda2-latest-Linux-x86_64.sh -b
# then add conda environ to you local enviroment.
# Please add:
# export PATH=PATH_TO_CONDA_BIN:$PATH
# to ~/.bashrc and then:
source ~/.bashrc

(conda config --add channels r)
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

2. Download the source code to local disk from the git directory
   

git clone https://github.com/adamtongji/rainbowRNA

3. Install CIRI2 in local if you want to run circRNA module
   

• CIRI2: "https://sourceforge.net/projects/ciri/files/CIRI2/"

4. Install the rainbowRNA
   

bash install.sh

5. (Recommend) Install the genome and annotation files from Illumina iGenomes
   The igenome website: iGenomes download page.
   

6. After installation, please check FAQ bug by test you conda and

library(clusterProfiler)

To test correct installation of R environment

Run the pipeline

rainbowRNA config_star.txt
# or
nohup rainbowRNA config_star.txt &

FAQ

1. Python2字符串编码报错。
   If occurs with following error:
   

if not line or line.startswith('#'):
   UnicodeDecodeError:
   'ascii' codec can't decode byte 0xe7 in position 50: ordinal not in range(128)

Please add following code to the script file "YOUPATH"/miniconda2/lib/python2.7/site-packages/conda/cli/common.py

reload(sys)
sys.setdefaultencoding('utf8')

Just add these code below "import sys" to avoid encoding error.

2. conda多个channel间不支持报错。
   If occurs with following error:
   

错误: package or namespace load failed for ‘stringi’
in dyn.load(file, DLLpath = DLLpath, ...):

Please run R in "rainbow_env", and re-install "stringi" after installation
as following code:

source activate rainbow_env
R

install.packages("stringi",dep=T)

其他错误请在issue中留言
个人主页: adamtongji.github.io