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
date Wed, 11 Oct 2017 15:06:20 -0400
parents fe5f30584308
children a709a705ce09
comparison
equal deleted inserted replaced
15:fe5f30584308 16:c2150a0f9c7c
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