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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty
author mingchen0919
date Tue, 17 Oct 2017 14:09:01 -0400
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-1:000000000000 0:512d008295db
1 ---
2 title: 'Download with BDSS client'
3 output:
4 html_document:
5 number_sections: true
6 toc: true
7 theme: cosmo
8 highlight: tango
9 ---
10
11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
12 knitr::opts_chunk$set(
13 echo = ECHO,
14 error=TRUE
15 )
16 ```
17
18 # Command line arguments
19
20 ```{r 'command line arguments'}
21 str(opt)
22 ```
23
24 # BDSS configuration file
25
26 First, we create a bdss configuration file `bdss.cfg` in the current directory.
27
28 ```{r}
29 system('echo "[metadata_repository]" > bdss.cfg')
30 system('echo url=http://bdss.bioinfo.wsu.edu/ >> bdss.cfg')
31 ```
32
33 # Download data
34
35 ```{r 'download and extract reads'}
36 # create a directory to store read files
37 dir.create('read_files_directory')
38 # download and extract reads
39 urls = strsplit(gsub(',', ' ', 'URLS'), ' ')[[1]]
40 urls = urls[urls != '']
41 # loop through SRA accessions to download and extract reads.
42 for(url in urls) {
43 print(url)
44 bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer --destination read_files_directory -u ', url)
45 print(bdss_command)
46 print(system(bdss_command, intern = TRUE))
47 }
48 # all files that need to be saved should be moved to REPORT_DIR directory
49 # print(system('mv read_files_directory REPORT_DIR', intern = TRUE))
50 ```
51
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