comparison bdss_client.Rmd @ 23:fd15cf620d5d draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 3d2a2c46f10b7f00a36771d2a0fc334d2c177730-dirty
author mingchen0919
date Sun, 15 Oct 2017 00:50:10 -0400
parents a709a705ce09
children a1c0ebd05f2f
comparison
equal deleted inserted replaced
22:89cc5b026494 23:fd15cf620d5d
39 urls = strsplit(gsub(',', ' ', 'URLS'), ' ')[[1]] 39 urls = strsplit(gsub(',', ' ', 'URLS'), ' ')[[1]]
40 urls = urls[urls != ''] 40 urls = urls[urls != '']
41 # loop through SRA accessions to download and extract reads. 41 # loop through SRA accessions to download and extract reads.
42 for(url in urls) { 42 for(url in urls) {
43 print(url) 43 print(url)
44 bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer --destination read_files_directory -u ', url) 44 bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer --destination read_files_directory -u ', url)
45 print(bdss_command) 45 print(bdss_command)
46 print(system(bdss_command, intern = TRUE)) 46 print(system(bdss_command, intern = TRUE))
47 } 47 }
48 # all files that need to be saved should be moved to REPORT_DIR directory 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)) 49 # print(system('mv read_files_directory REPORT_DIR', intern = TRUE))