Mercurial > repos > mingchen0919 > rmarkdown_bdss_client
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 |
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date | Sun, 15 Oct 2017 00:50:10 -0400 |
parents | a709a705ce09 |
children | a1c0ebd05f2f |
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22:89cc5b026494 | 23:fd15cf620d5d |
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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)) |