Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

diff bdss_client_sra.Rmd @ 29:69d51de74c0f draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 7c282211dbff8125b5aeef6e0172d5eb2f3a2ddb-dirty
author mingchen0919
date Mon, 16 Oct 2017 23:55:36 -0400
parents 3764ba86f0da
children
line wrap: on
line diff
--- a/bdss_client_sra.Rmd	Mon Oct 16 23:34:33 2017 -0400
+++ b/bdss_client_sra.Rmd	Mon Oct 16 23:55:36 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') {
@@ -68,7 +68,7 @@
                  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') {