Mercurial > repos > mingchen0919 > aurora_bdss
changeset 2:845f4b9d7cf3 draft default tip
planemo upload commit 602f5b82864867a81c2e4ea2be9b52f4b635bd7b-dirty
| author | mingchen0919 |
|---|---|
| date | Wed, 30 May 2018 19:52:36 -0400 |
| parents | 8b0ac9578ad4 |
| children | |
| files | rmarkdown_report.Rmd rmarkdown_report.xml |
| diffstat | 2 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/rmarkdown_report.Rmd Tue May 29 09:08:00 2018 -0400 +++ b/rmarkdown_report.Rmd Wed May 30 19:52:36 2018 -0400 @@ -80,7 +80,7 @@ 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/test-galaxy/tools/_conda/bin/bdss transfer -u ', url) system(bdss_command, intern = TRUE) # convert .sra to .fastq/.fasta if('FORMAT' == 'fasta') { @@ -102,7 +102,7 @@ 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/test-galaxy/tools/_conda/bin/bdss transfer -u ', url) system(bdss_command, intern = TRUE) # convert .sra to .fastq/.fasta if(opt$X_f == 'fasta') {
--- a/rmarkdown_report.xml Tue May 29 09:08:00 2018 -0400 +++ b/rmarkdown_report.xml Wed May 30 19:52:36 2018 -0400 @@ -6,6 +6,7 @@ <requirement type="package" version="1.15.0.6-0">pandoc</requirement> <requirement type="package" version="1.20.0">r-getopt</requirement> <requirement type="package" version="1.6">r-rmarkdown</requirement> + <requirement type="package" version="0.6.2">parallel-fastq-dump</requirement> </requirements> <command><![CDATA[