Mercurial > repos > mingchen0919 > aurora_bdss_sra

diff rmarkdown_report.Rmd @ 1:bd236d81187b draft

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planemo upload for repository https://github.com/feltus/BDSS
author mingchen0919
date Tue, 12 Jun 2018 09:35:23 -0400
parents 759232961286
children cf17a4199861
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--- a/rmarkdown_report.Rmd	Tue Jun 12 09:24:06 2018 -0400
+++ b/rmarkdown_report.Rmd	Tue Jun 12 09:35:23 2018 -0400
@@ -61,7 +61,9 @@
 pe_dir = paste0(Sys.getenv('JOB_WORKING_DIR'), '/pe_read_files_dir')
 ```
 
-```{r 'download and extract reads'}
+```{r 'download and extract reads', echo=-1}
+Sys.setenv(PATH=paste0('/main/sites/galaxy/galaxy/tools/_conda/bin:', Sys.getenv('PATH')))
+
 # download and extract reads (single end)
 sra_ids_se = strsplit(gsub(',', ' ', 'SRA_IDS_SE'), ' ')[[1]]
 sra_ids_se = sra_ids_se[sra_ids_se != '']