add zenodo doi

DESCRIPTION

@@ -4,7 +4,7 @@ Version: 0.3.5
 Authors@R: person("Jianfeng", "Li", email = "lee_jianfeng@sjtu.edu.cn", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2349-208X"))
 Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
 Description:
-    Can be used to integrate massive bioinformatics tool/script and database. It provides the R, Shiny web application, and the GitHub forum. Hundreds of bioinformatics tool/script and database have been included in BioInstaller.
+    Can be used to integrate massive bioinformatics tool/script and database. It provides the R, Shiny web application, and the github forum. Hundreds of bioinformatics tool/script and database have been included.
 Depends:
     R (>= 3.3.0)
 URL: https://github.com/JhuangLab/BioInstaller

README.md

@@ -3,6 +3,7 @@
 [![Build
 Status](https://travis-ci.org/JhuangLab/BioInstaller.svg)](https://travis-ci.org/JhuangLab/BioInstaller)
 [![CRAN](http://www.r-pkg.org/badges/version/BioInstaller)](https://cran.r-project.org/package=BioInstaller)
+[![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.1343914.svg)](https://zenodo.org/record/1343914)
 [![Downloads](http://cranlogs.r-pkg.org/badges/BioInstaller?color=brightgreen)](http://www.r-pkg.org/pkg/BioInstaller)
 [![codecov](https://codecov.io/github/JhuangLab/BioInstaller/branch/master/graphs/badge.svg)](https://codecov.io/github/JhuangLab/BioInstaller)
 
@@ -56,13 +57,26 @@ It provides the R, Shiny web application, and the GitHub forum. Hundreds of bioi
 
 <img src="https://raw.githubusercontent.com/JhuangLab/BioInstaller/develop/man/figures/design_of_bioInstaller.jpg" align="middle" />
 
+## Installation
+
+### CRAN
+
+``` r
+#You can install this package directly from CRAN by running (from within R):
+install.packages('BioInstaller')
+```
 
+### Github
+
+``` bash
+# install.packages("devtools")
+devtools::install_github("JhuangLab/BioInstaller")
+
+```
 ## Shiny UI overview
 
 ```
-# install the latest developmental version
-# than start the BioInstaller R Shiny application
-# the document is still under construction
+# Start the standalone Shiny application
 BioInstaller::web()
 ```
 
@@ -76,21 +90,6 @@ BioInstaller::web()
 
 <img src="https://raw.githubusercontent.com/Miachol/ftp/master/files/images/bioinstaller/overview5.jpg" align="middle" />
 
-## Installation
-
-### CRAN
-
-``` r
-#You can install this package directly from CRAN by running (from within R):
-install.packages('BioInstaller')
-```
-
-### Github
-
-``` bash
-# install.packages("devtools")
-devtools::install_github("JhuangLab/BioInstaller")
-```
 
 ## Contributed Resources
 
@@ -163,9 +162,9 @@ docker run -it -p 80:80 -p 8004:8004 -v /tmp/download:/tmp/download bioinstaller
 
 Service list:
 
-- http://localhost/ocpu/ Opencpu service
-- http://localhost/shiny/BioInstaller Shiny service
-- http://localhost/rstudio/ Rstudio server (opencpu/opencpu)
+- localhost/ocpu/ Opencpu service
+- localhost/shiny/BioInstaller Shiny service
+- localhost/rstudio/ Rstudio server (opencpu/opencpu)
 
 ## How to contribute?
 

vignettes/start_shiny_of_BioInstaller.Rmd

@@ -35,9 +35,9 @@ docker run -it -p 80:80 -p 8004:8004 -v /tmp/download:/tmp/download bioinstaller
 
 When the docker container of BioInstaller was created, you can access the three types of web service in the browser.
 
-- http://localhost/ocpu/ Opencpu server
-- http://localhost/shiny/BioInstaller Shiny server
-- http://localhost/rstudio/ Rstudio server (opencpu/opencpu)
+- localhost/ocpu/ Opencpu server
+- localhost/shiny/BioInstaller Shiny server
+- localhost/rstudio/ Rstudio server (opencpu/opencpu)
 
 ### Opencpu server