Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

changeset 16:c2150a0f9c7c draft

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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 246cb7315673
files bdss_client.Rmd bdss_client_sra_pe.Rmd bdss_client_sra_se.Rmd
diffstat 3 files changed, 9 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/bdss_client.Rmd	Wed Oct 11 14:50:19 2017 -0400
+++ b/bdss_client.Rmd	Wed Oct 11 15:06:20 2017 -0400
@@ -39,8 +39,7 @@
 urls = urls[urls != '']
 # loop through SRA accessions to download and extract reads.
 for(url in urls) {
-    # bdss_command = paste0('cd ./read_files_directory && /tool_deps/_conda/bin/bdss transfer -u ', url)
-    bdss_command = paste0('cd ./read_files_directory && /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
+    bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer --destination read_files_directory -u ', url)
     print(system(bdss_command, intern = TRUE))
 }
 ```
--- a/bdss_client_sra_pe.Rmd	Wed Oct 11 14:50:19 2017 -0400
+++ b/bdss_client_sra_pe.Rmd	Wed Oct 11 15:06:20 2017 -0400
@@ -37,7 +37,7 @@
                  substr(id, 1, 3), '/',
                  substr(id, 1, 6), '/', id, '/', id, '.sra')
     # download sra file with bdss
-    bdss_command = paste0(' /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
+    bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
     system(bdss_command, intern = TRUE)
     # convert .sra to .fastq/.fasta
     if('FORMAT' == 'fasta') {
@@ -59,17 +59,17 @@
       print(paste0('only one fastq file found for this SRA accession: ', id))
       print(paste0('Downloading skipped for ', id))
       # url = paste0(url_base, '/', all_fastq_files)
-      # bdss_command = paste0(' /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
+      # bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
       # run_bdss = system(bdss_command, intern = TRUE)
       # print(run_bdss)
     } else {
       print(paste0('Two fastq files found for this SRA accession: ', id))
       url_1 = paste0(url_base, '/', all_fastq_files[1])
-      bdss_command_1 = paste0(' /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url_1)
+      bdss_command_1 = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url_1)
       run_bdss_1 = system(bdss_command_1, intern = TRUE)
       print(run_bdss_1)
       url_2 = paste0(url_base, '/', all_fastq_files[1])
-      bdss_command_2 = paste0(' /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url_2)
+      bdss_command_2 = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url_2)
       run_bdss_2 = system(bdss_command_2, intern = TRUE)
       print(run_bdss_2)
     }
--- a/bdss_client_sra_se.Rmd	Wed Oct 11 14:50:19 2017 -0400
+++ b/bdss_client_sra_se.Rmd	Wed Oct 11 15:06:20 2017 -0400
@@ -46,7 +46,7 @@
                  substr(id, 1, 3), '/',
                  substr(id, 1, 6), '/', id, '/', id, '.sra')
     # download sra file with bdss
-    bdss_command = paste0(' /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
+    bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
     system(bdss_command, intern = TRUE)
     # convert .sra to .fastq/.fasta
     if('FORMAT' == 'fasta') {
@@ -64,17 +64,17 @@
     if (length(all_fastq_files) == 1) {
       # this is a single end SRA file. build url to download fastq
       url = paste0(url_base, '/', all_fastq_files)
-      bdss_command = paste0(' /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
+      bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
       run_bdss = system(bdss_command, intern = TRUE)
       print(run_bdss)
     } else {
       print(paste0('Two fastq files found for this SRA accession: ', id))
       print('Downloading skipped for ', id)
       # url_1 = paste0(url_base, '/', all_fastq_files[1])
-      # bdss_command_1 = paste0(' /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url_1)
+      # bdss_command_1 = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url_1)
       # run_bdss_1 = system(bdss_command, intern = TRUE)
       # url_2 = paste0(url_base, '/', all_fastq_files[1])
-      # bdss_command_2 = paste0(' /main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url_2)
+      # bdss_command_2 = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url_2)
       # run_bdss_2 = system(bdss_command, intern = TRUE)
     }
   }