replaced dropbox links to core_* with versioned github links

chipseq_workflow/chipseq_utils.sh

@@ -108,8 +108,8 @@ done
 wait
 
 echo '
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.5/R/core_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.5/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")
 
 libSizes <- read.delim("algn_counts.txt", header=F) %>% set_names(c("library_size", "sample"))
 libSizes %>% ggplot(aes(sample, library_size)) +

dge_workflow/cutadapt_summary.R

@@ -4,8 +4,8 @@
 
 ## Note This script is supposed to be knitr::spin'ed
 
-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(knitr)
 
 ## can we access variables from the parent spin.R process?

dge_workflow/dge_analysis.R

@@ -39,9 +39,9 @@ if(is.na(file.info(cuffdb_directory)$isdir)){
 }
 
 
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.5/R/core_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.5/R/ggplot_commons.R")
-devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.5/R/bio/diffex_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")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/bio/diffex_commons.R")
 
 require(cummeRbund)
 

dge_workflow/dge_utils.sh

@@ -2,7 +2,7 @@
 ## http://blog.joncairns.com/2013/08/what-you-need-to-know-about-bash-functions/
 
 ## load lsf helpers
-source <(curl https://dl.dropboxusercontent.com/u/113630701/datautils/bash/lsf_utils.sh 2>&1 2>/dev/null)
+source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/bash/lsf_utils.sh 2>&1 2>/dev/null)
 
 ## enable snippet spinning
 source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/master/R/spinr/spin_utils.sh 2>&1 2>/dev/null)

dge_workflow/fastqc_summary.R

@@ -4,8 +4,8 @@
 
 ## Note This script is supposed to be knitr::spin'ed
 
-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")
 
 ## can we access variables from the parent spin.R process?
 #echo("rscript is ", r_script)

dge_workflow/tophat_qc.R

@@ -26,8 +26,8 @@ if(is.na(file.info(baseDir)$isdir)){
     stop(paste("base directory", baseDir, "does not exist"))
 }
 
-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")
 
 
 ########################################################################################################################