Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

diff bdss_client_sra.Rmd @ 25:821832531529 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit b212086a85c4d1e62e0d0c0e77b6f3fcabea04ef-dirty
author mingchen0919
date Sun, 15 Oct 2017 22:38:29 -0400
parents a1c0ebd05f2f
children fb8f1d1ceeae
line wrap: on
line diff
--- a/bdss_client_sra.Rmd	Sun Oct 15 01:00:51 2017 -0400
+++ b/bdss_client_sra.Rmd	Sun Oct 15 22:38:29 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('/tool_deps/_conda/bin/bdss transfer -u ', url)
+    bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_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('/tool_deps/_conda/bin/bdss transfer -u ', url)
+    bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url)
     system(bdss_command, intern = TRUE)
     # convert .sra to .fastq/.fasta
     if('FORMAT' == 'fasta') {