Commit 42913ddd authored by Holger Brandl's avatar Holger Brandl

replaced dropbox links to core_* with versioned github links

parent 09860411
......@@ -29,7 +29,7 @@ rknit(){
# cat $rscript | grep -Fv '#!' | Rscript --vanilla -e 'source("/Users/brandl/Dropbox/Public/datautils/R/rknit/rknit_preprocessor.R")' >> $tmpRmd
# cat $rscript | sed 's/^#>$//g'| grep -Fv '#!' | Rscript --vanilla -e 'devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/master/R/rknit/rknit_preprocessor.R")' | grep -v "^#>" >> $tmpRmd
cat $rscript | sed 's/^#>$//g' | grep -Fv '#!'| grep -Ev '^#+$' | Rscript --vanilla -e 'devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/rknit/rknit_preprocessor.R")' >> $tmpRmd
cat $rscript | sed 's/^#>$//g' | grep -Fv '#!'| grep -Ev '^#+$' | Rscript --vanilla -e 'devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/rknit/rknit_preprocessor.R")' >> $tmpRmd
echo '```' >> $tmpRmd
......
......@@ -6,9 +6,6 @@
#https://github.com/edwindj/docopt.R
#http://www.slideshare.net/EdwindeJonge1/docopt-user2014
## a thin wrapper around spin to make it more useful with more custom output
#devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/core_commons.R")
# load the docopt library
suppressMessages(library(docopt))
......
......@@ -3,8 +3,8 @@
#sessionInfo()
devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/core_commons.R")
devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/ggplot_commons.R")
require.auto(lubridate)
......
......@@ -2,8 +2,8 @@
## Tophat Mapping Report from the logs
TophatMappingReport(){
echo '
devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/core_commons.R")
devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/ggplot_commons.R")
parseAlgnSummary_T2_0_11 <- function(alignSummary){
......@@ -53,8 +53,8 @@ export -f TophatMappingReport
#Bowtie2MappingReport(){
#
#echo '
#devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/core_commons.R")
#devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/ggplot_commons.R")
#devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/core_commons.R")
#devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/ggplot_commons.R")
#
#logSuffix=".logs"
#parseAlgnSummary <- function(alignSummary){
......@@ -94,7 +94,7 @@ MakeCuffDB() {
if [ $# -ne 2 ]; then echo "Usage: MakeCuffDB <gtffile> <genomebuild>"; return; fi
echo '
devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/core_commons.R")
require.auto(cummeRbund)
......
......@@ -72,12 +72,12 @@ jlistReport(){
# ## add spin.R
# export PATH=/projects/bioinfo/holger/bioinfo_templates/misc:$PATH
# source $(which spin_utils.sh)
wget wget https://dl.dropboxusercontent.com/u/113630701/datautils/bash/CreateJobReport.R
wget https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/bash/CreateJobReport.R
chmod u+x CreateJobReport.R
CreateJobReport.R $joblistFile
# echo "Creating report for $joblistFile"
# echo "reportName='$joblistFile'; devtools::source_url('https://dl.dropboxusercontent.com/u/113630701/datautils/bash/CreateJobReport.R',local=T)" | spinsnip $(echo $joblistFile | tr -d ".")
# echo "reportName='$joblistFile'; devtools::source_url('https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/bash/CreateJobReport.R',local=T)" | spinsnip $(echo $joblistFile | tr -d ".")
rm CreateJobReport.R
}
export -f jlistReport
......
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