Mercurial > repos > mingchen0919 > rmarkdown_bdss_client
comparison bdss_client.Rmd @ 16:c2150a0f9c7c draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
author | mingchen0919 |
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date | Wed, 11 Oct 2017 15:06:20 -0400 |
parents | fe5f30584308 |
children | a709a705ce09 |
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15:fe5f30584308 | 16:c2150a0f9c7c |
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37 # download and extract reads | 37 # download and extract reads |
38 urls = strsplit(gsub(',', ' ', 'URLS'), ' ')[[1]] | 38 urls = strsplit(gsub(',', ' ', 'URLS'), ' ')[[1]] |
39 urls = urls[urls != ''] | 39 urls = urls[urls != ''] |
40 # loop through SRA accessions to download and extract reads. | 40 # loop through SRA accessions to download and extract reads. |
41 for(url in urls) { | 41 for(url in urls) { |
42 # bdss_command = paste0('cd ./read_files_directory && /tool_deps/_conda/bin/bdss transfer -u ', url) | 42 bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer --destination read_files_directory -u ', url) |
43 bdss_command = paste0('cd ./read_files_directory && /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url) | |
44 print(system(bdss_command, intern = TRUE)) | 43 print(system(bdss_command, intern = TRUE)) |
45 } | 44 } |
46 ``` | 45 ``` |
47 | 46 |
48 | 47 |