Mercurial > repos > mingchen0919 > aurora_bdss_url
changeset 7:86f38533b2ab draft
planemo upload for repository https://github.com/feltus/BDSS
author | mingchen0919 |
---|---|
date | Tue, 12 Jun 2018 00:54:24 -0400 |
parents | af2e4c66261f |
children | f7bd614bdb68 |
files | build-and-run-job-scripts.sh rmarkdown_report.xml rmarkdown_report_render.R |
diffstat | 3 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/build-and-run-job-scripts.sh Tue Jun 12 00:15:20 2018 -0400 +++ b/build-and-run-job-scripts.sh Tue Jun 12 00:54:24 2018 -0400 @@ -1,6 +1,3 @@ -# create a download_dir in current job working directory -JOB_WORKING_DIR=$(pwd) - # run job scripts within the tool outputs directory cd ${REPORT_FILES_PATH} mkdir download_dir @@ -11,7 +8,8 @@ echo 'do' >> bdss-download.sh echo ' bdss transfer --destination download_dir -u $u' >> bdss-download.sh echo 'done' >> bdss-download.sh +echo 'echo $(pwd)' >> bdss-download.sh sh bdss-download.sh - -cp -r download_dir ${JOB_WORKING_DIR}/download_dir \ No newline at end of file +# copy data from REPORT_FILES_PATHS to JOB_WORKING_DIR so that files can be discovered automatically. +cp -r download_dir ${JOB_WORKING_DIR} \ No newline at end of file
--- a/rmarkdown_report.xml Tue Jun 12 00:15:20 2018 -0400 +++ b/rmarkdown_report.xml Tue Jun 12 00:54:24 2018 -0400 @@ -38,7 +38,7 @@ help="Multiple URLs should be separated with comma or space"/> </inputs> <outputs> - <data format="html" name="report" label="${tool.name} report on ${on_string}"/> + <data format="html" name="report" label="${tool.name} report"/> <data name="output" label="BDSS downloaded data"> <discover_datasets pattern="__name_and_ext__" directory="download_dir" visible="true"/> </data>
--- a/rmarkdown_report_render.R Tue Jun 12 00:15:20 2018 -0400 +++ b/rmarkdown_report_render.R Tue Jun 12 00:54:24 2018 -0400 @@ -109,6 +109,8 @@ # define environment variables for all input values. this is useful when we # want to use input values by other programming language in r markdown do.call(Sys.setenv, opt[-1]) +# add current job working directory +Sys.setenv(JOB_WORKING_DIR=getwd()) #===============================================================