Mercurial > repos > mingchen0919 > rmarkdown_bdss_client
changeset 29:69d51de74c0f draft
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 | e97a8e2b8183 |
| files | bdss_client.Rmd bdss_client.xml bdss_client_sra.Rmd bdss_client_sra.xml |
| diffstat | 4 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/bdss_client.Rmd Mon Oct 16 23:34:33 2017 -0400 +++ b/bdss_client.Rmd Mon Oct 16 23:55:36 2017 -0400 @@ -41,7 +41,7 @@ # loop through SRA accessions to download and extract reads. for(url in urls) { print(url) - bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer --destination read_files_directory -u ', url) + bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer --destination read_files_directory -u ', url) print(bdss_command) print(system(bdss_command, intern = TRUE)) }
--- a/bdss_client.xml Mon Oct 16 23:34:33 2017 -0400 +++ b/bdss_client.xml Mon Oct 16 23:55:36 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="rmarkdown_bdss_client" name="BDSS client" version="1.0.3"> +<tool id="rmarkdown_bdss_client" name="BDSS client" version="1.0.4"> <requirements> <requirement type="package" version="1.15.0.6-0">pandoc</requirement> <requirement type="package" version="3.3.2">r-base</requirement>
--- 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') {
--- a/bdss_client_sra.xml Mon Oct 16 23:34:33 2017 -0400 +++ b/bdss_client_sra.xml Mon Oct 16 23:55:36 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="rmarkdown_bdss_client_sra" name="BDSS client SRA" version="1.0.3"> +<tool id="rmarkdown_bdss_client_sra" name="BDSS client SRA" version="1.0.4"> <requirements> <requirement type="package" version="1.15.0.6-0">pandoc</requirement> <requirement type="package" version="3.3.2">r-base</requirement>