Commit 94af8065 authored by brandl's avatar brandl

removed gh with gitlab paths in source_url calls

parent bf8e86fe
......@@ -26,7 +26,7 @@ opts <- docopt(doc, commandArgs(TRUE))
#opts <- docopt(doc, "H3HA_Dome.narrow_summits.bam,H3HA_Oblong.narrow_summits.bam,H3HA_Sphere.narrow_summits.bam,K4M_Dome.narrow_summits.bam,K4M_Oblong.narrow_summits.bam,K4M_Sphere.narrow_summits.bam tss,genebody")
#opts <- docopt(doc, "--print_cmd_only H3HA_Dome.narrow_summits.bam,H3HA_Oblong.narrow_summits.bam,H3HA_Sphere.narrow_summits.bam,K4M_Dome.narrow_summits.bam,K4M_Oblong.narrow_summits.bam,K4M_Sphere.narrow_summits.bam tss,genebody")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.13/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.13/R/core_commons.R")
require.auto(whisker) # http://stackoverflow.com/questions/10341114/alternative-function-to-paste
......
......@@ -24,8 +24,8 @@ if(is.na(file.info(baseDir)$isdir)){
stop(paste("base directory", baseDir, "does not exist"))
}
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/core_commons.R")
#devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.26/R/core_commons.R")
#devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.26/R/ggplot_commons.R")
########################################################################################################################
......
source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.50/tools/rendr/rendr_utils.sh 2>&1 2>/dev/null)
#source <(curl https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.50/tools/rendr/rendr_utils.sh 2>&1 2>/dev/null)
source <(curl https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.50/tools/rendr/rendr_utils.sh 2>&1 2>/dev/null)
source <(curl https://git.mpi-cbg.de/bioinfo/ngs_tools/raw/v10/common/bash_utils.sh 2>&1 2>/dev/null)
## configure paths
#python setup_w_cython.py install --prefix /home/brandl/bin/macs2
## todo use append2path as for dge_utils
export PATH=/projects/bioinfo/holger/bin/bedtools2-2.25.0/bin:${PATH}
export PATH=/home/brandl/bin/macs2/bin:${PATH}
export PYTHONPATH=/home/brandl/bin/macs2/lib:$PYTHONPATH
......@@ -17,8 +18,8 @@ export PYTHONPATH=/home/brandl/bin/macs2/lib/python2.7/site-packages:$PYTHONPATH
cs_bowtie_qc(){
rendr_snippet "bowtie2_qc" <<"EOF"
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.8/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.8/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.8/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.8/R/ggplot_commons.R")
########################################################################################################################
#> # Bowtie2 Mapping Summary
......@@ -113,8 +114,8 @@ done
wait
echo '
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.26/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.26/R/ggplot_commons.R")
libSizes <- read_tsv("algn_counts.txt", col_names=F) %>% set_names(c("library_size", "sample"))
libSizes %>% ggplot(aes(sample, library_size)) +
......@@ -138,7 +139,7 @@ if [ $# -ne 2 ]; then
fi
echo '
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.38/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.38/R/core_commons.R")
bamFile=commandArgs(T)[1]
chromInfoFile=commandArgs(T)[2]
......@@ -181,7 +182,7 @@ if [ $# -ne 2 ]; then
fi
echo '
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.38/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.38/R/core_commons.R")
chromInfo=commandArgs(T)[1]
bedFile=commandArgs(T)[2]
......
#!/usr/bin/env Rscript
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.4/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.4/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/master/R/bio/diffex_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.4/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.4/R/ggplot_commons.R")
## todo replace with ngs_tools/dge_workflow/diffex_commons.R
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.40/R/bio/diffex_commons.R")
require(tidyr)
......
......@@ -15,10 +15,10 @@ Options:
opts = docopt(doc, commandArgs(TRUE))
# devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.50/R/core_commons.R")
# devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.50/R/core_commons.R")
devtools::source_url("https://dl.dropboxusercontent.com/s/rwnpjpfz0aa9zg0/core_commons.R?dl=0")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.50/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.50/R/ggplot_commons.R")
##todo port back into core_commons
# set_names <- purrr::set_names
......
......@@ -25,8 +25,8 @@ ensVersion <- opts$ens_archive
species <- opts$species
sloping <- opts$sloping
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R//core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R//bio/bioinfo_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.22/R//core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.22/R//bio/bioinfo_commons.R")
require_auto(whisker) # http://stackoverflow.com/questions/10341114/alternative-function-to-paste
#?whisker.render
......
......@@ -21,10 +21,10 @@ Options:
opts <- docopt(doc, commandArgs(TRUE)) ## does not work when spining
# opts <- docopt(doc, "--overlay_expr_data ../plot_score_matrix.txt ../degs_by_contrast.txt contrast" )
coreCommons = "https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/core_commons.R"
coreCommons = "https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/core_commons.R"
devtools::source_url(coreCommons)
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/ngs_tools/raw/v6/common/cp_utils.R")
# source(interp_from_env("${NGS_TOOLS}/common/cp_utils.R"))
......@@ -35,7 +35,7 @@ devtools::source_url("https://git.mpi-cbg.de/bioinfo/ngs_tools/raw/v6/dge_workfl
# should be no longer needed
# devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.44/R/bio/diffex_commons.R")
# devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.44/R/bio/diffex_commons.R")
# devtools::source_url("https://www.dropbox.com/s/vkmm66n11qyunma/diffex_commons.R?dl=1")
......
......@@ -165,7 +165,7 @@ cp_test = function(geneIds, annoDb, cp_species, q_cutoff=0.05){
## example usage
if(F){
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.33/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.33/R/core_commons.R")
devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/bio/cp_utils.R")
......@@ -197,10 +197,10 @@ if(F){
### Yeast Example
if(F){
# devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.42/R/core_commons.R")
# devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.42/R/core_commons.R")
devtools::source_url("https://www.dropbox.com/s/r6kim8kb8ohmptx/core_commons.R?dl=1")
# devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.42/R/bio/cp_utils.R")
# devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.42/R/bio/cp_utils.R")
devtools::source_url("https://www.dropbox.com/s/p2b8luxf7jteb63/cp_utils.R?dl=1")
......
......@@ -17,8 +17,8 @@ Options:
opts <- docopt(doc, commandArgs(TRUE)) ## does not work when spining
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/ngs_tools/raw/v6/common/cp_utils.R")
# source(interp_from_env("${NGS_TOOLS}/common/cp_utils.R"))
......
......@@ -18,11 +18,11 @@ Options:
opts = docopt(doc, commandArgs(TRUE)) ## does not work when spining
# opts = docopt(doc, "--overlay_expr_data ../plot_score_matrix.txt ../degs_by_contrast.txt contrast" )
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.40/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.40/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.40/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.40/R/bio/diffex_commons.R")
# devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.40/R/bio/cp_utils.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.40/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.40/R/bio/diffex_commons.R")
# devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.40/R/bio/cp_utils.R")
# devtools::source_url("https://www.dropbox.com/s/p2b8luxf7jteb63/cp_utils.R?dl=1")
......
......@@ -20,10 +20,10 @@ Options:
opts <- docopt(doc, commandArgs(TRUE)) ## does not work when spining
# opts <- docopt(doc, "--overlay_expr_data ../plot_score_matrix.txt ../degs_by_contrast.txt contrast" )
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.27/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.27/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.27/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.27/R/ggplot_commons.R")
## todo relase and use proper version here
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/master/R/bio/diffex_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/master/R/bio/diffex_commons.R")
loadpack(knitr)
#loadpack(DT)
......
......@@ -8,7 +8,7 @@ cd /projects/bioinfo/igenomes
#export NGS_TOOLS=/net/mack/lustre/projects/bioinfo/brandl/scripts/ngs_tools/
export NGS_TOOLS="/projects/bioinfo/$(whoami)/scripts/ngs_tools"
source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.42/bash/core_utils.sh 2>&1 2>/dev/null)
source <(curl https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.42/bash/core_utils.sh 2>&1 2>/dev/null)
......
#!/usr/bin/env Rscript
#+ echo=FALSE
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/bio/diffex_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/bio/diffex_commons.R")
require(reshape)
library(splitstackshape)
......
......@@ -14,9 +14,9 @@ opts <- docopt(doc, commandArgs(TRUE)) ## does not work when spining
# opts <- docopt(doc, "--overlay_expr_data ../plot_score_matrix.txt ../degs_by_contrast.txt contrast" )
if(!require(devtools)) install.packages("devtools")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/core_commons.R")
# devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/bio/diffex_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/core_commons.R")
# devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/bio/diffex_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/ngs_tools/raw/v6/common/cp_utils.R")
load_pack(knitr)
......
......@@ -19,7 +19,7 @@ opts = docopt(doc, commandArgs(TRUE))
# LOAD packages -------------------------------------------------------------------------------
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.47/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.47/R/core_commons.R")
# source("http://bioconductor.org/biocLite.R")
# biocLite("pachterlab/sleuth")
# source("https://bioconductor.org/biocLite.R")
......
......@@ -19,8 +19,8 @@ opts = docopt(doc, commandArgs(TRUE))
# LOAD packages -------------------------------------------------------------------------------
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.43/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.40/R/bio/diffex_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.43/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.40/R/bio/diffex_commons.R")
install_package("biomaRt")
load_pack(knitr)
......
......@@ -49,9 +49,9 @@ if(is.na(file.info(cuffdb_directory)$isdir)){
}
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/bio/diffex_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/bio/diffex_commons.R")
#+ results='asis', echo=FALSE
cat('
......
......@@ -49,9 +49,9 @@ if(is.na(file.info(cuffdb_directory)$isdir)){
}
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/bio/diffex_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/bio/diffex_commons.R")
#+ results='asis', echo=FALSE
cat('
......
......@@ -4,8 +4,8 @@
## Note This script is supposed to be knitr::spin'ed
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.46/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.46/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.46/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.46/R/ggplot_commons.R")
load_pack(knitr)
## can we access variables from the parent spin.R process?
......
......@@ -4,8 +4,8 @@
## Note This script is supposed to be knitr::spin'ed
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.46/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.46/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.46/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.46/R/ggplot_commons.R")
load_pack(knitr)
## can we access variables from the parent spin.R process?
......
......@@ -52,7 +52,7 @@ dge_fastqc $(ls *fastq.gz) &
mcdir $baseDir/lanereps_pooled
echo '
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.10/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.10/R/core_commons.R")
options(java.parameters = "-Xmx4g" ); library(xlsx)
......
......@@ -26,8 +26,8 @@ if(is.na(file.info(baseDir)$isdir)){
stop(paste("base directory", baseDir, "does not exist"))
}
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://git.mpi-cbg.de/bioinfo/datautils/raw/v1.9/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.9/R/ggplot_commons.R")
########################################################################################################################
......
......@@ -39,9 +39,9 @@ if(is.na(file.info(cuffdb_directory)$isdir)){
}
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")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.9/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.9/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.9/R/bio/diffex_commons.R")
require(cummeRbund)
......
......@@ -90,7 +90,7 @@ rendr_snippet "duplicate_analysis" <<"EOF" $gtfFile ${outputDir}/*.markdup.bam
#' Working directory: `r getwd()`
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.40/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.40/R/core_commons.R")
load_pack(dupRadar)
# source("https://bioconductor.org/biocLite.R")
......
......@@ -23,8 +23,8 @@ opts = docopt(doc, commandArgs(TRUE))
## load some packages first because of name-space order
library(knitr)
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.46/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.46/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.46/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.46/R/ggplot_commons.R")
load_pack(glue)
load_pack(htmltools)
......
......@@ -15,7 +15,7 @@ Options
opts = docopt(doc, commandArgs(TRUE)) ## does not work when spining
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.46/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.46/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/ngs_tools/raw/v8/dge_workflow/diffex_commons.R")
......
......@@ -66,7 +66,7 @@ dge_fastqc $(ls *fastq.gz) &
mcdir ${PRJ_DATA}/lanereps_pooled
echo '
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.42/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.42/R/core_commons.R")
sheetFile <- "../originals/natalied-FC_SN678_338-2015-5-12.xls"
......@@ -156,7 +156,7 @@ mcdir ${PRJ_DATA}/dge_analysis
## build custom design matrix
#csvcut -tc replicate,sample $baseDir/lanereps_pooled/renaming_scheme.txt | csvformat -T > design_matrix.txt
#Rscript - <<"EOF"
#devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.36/R/core_commons.R")
#devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.36/R/core_commons.R")
#file.path(Sys.getenv("baseDir"), "lanereps_pooled/renaming_scheme.txt") %>%
# read_tsv() %>%
# distinct(replicate, sample) %>%
......
......@@ -50,7 +50,7 @@ export PATH=/home/$(whoami)/.local/bin:$PATH
append2path ${BIO_BIN_BASE}/joblist_v0.7.1
## make sure that rend.R is present
source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.50/tools/rendr/rendr_utils.sh 2>&1 2>/dev/null)
source <(curl https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.50/tools/rendr/rendr_utils.sh 2>&1 2>/dev/null)
source <(curl https://git.mpi-cbg.de/bioinfo/ngs_tools/raw/v10/common/bash_utils.sh 2>&1 2>/dev/null)
......@@ -358,7 +358,7 @@ export -f dge_get_pc_isoforms
dge_star_counts2matrix(){
echo '
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.40/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.40/R/core_commons.R")
## STAR count file format is
#column 1: gene ID
......
......@@ -12,7 +12,7 @@
args = commandArgs(trailingOnly = TRUE)
# LOAD packages --------------------------------------------------------------------------------------------------------
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.44/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.44/R/core_commons.R")
load_pack(shiny)
load_pack(shinyFiles)
load_pack(DT)
......
......@@ -59,8 +59,8 @@ library(DESeq2)
library(IHW)
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/ggplot_commons.R")
## also load common helper for expression data analysis
# source(interp_from_env("${NGS_TOOLS}/dge_workflow/diffex_commons.R"))
......
......@@ -29,8 +29,8 @@ opts = docopt(doc, commandArgs(TRUE))
## load some packages first because of name-space order
library(knitr)
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.49/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.49/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.49/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.49/R/ggplot_commons.R")
## also load common helper for expression data analysis
# source(interp_from_env("${NGS_TOOLS}/dge_workflow/diffex_commons.R"))
......
......@@ -43,7 +43,7 @@ mailme "dupradar refs done"
## integrate stats for report overlay
rendr_snippet "dupstats_integration" <<"EOF"
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.39/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.39/R/core_commons.R")
EOF
......
......@@ -4,8 +4,8 @@
## Note This script is supposed to be knitr::spin'ed
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.9/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.9/R/ggplot_commons.R")
require(knitr)
## Can we access variables from the parent spin.R process?
......
......@@ -22,8 +22,8 @@ if(is.na(file.info(base_directory)$isdir)){
stop(paste("base directory", base_directory, "does not exist"))
}
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.22/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.22/R/ggplot_commons.R")
require_auto(knitr)
########################################################################################################################
......
......@@ -2,7 +2,7 @@
## madmax /sw/bin/Rscript
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.38/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.38/R/core_commons.R")
#library(RCurl, quietly=T, warn.conflicts=F)
#library(devtools) ## http?://stackoverflow.com/questions/7715723/sourcing-r-script-over-https
......
......@@ -16,9 +16,9 @@ opts <- docopt(doc, commandArgs(TRUE)) ## does not work when spining
#opts <- docopt(doc, "--overlay_expr_data ../ctrl_fc_expr_filtered.txt geneClusters.RData" )
#opts <- docopt(doc, "--overlay_expr_data ../ctrl_fc_expr_filtered.txt grpdGoiClusters.RData" )
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/bio/diffex_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/bio/diffex_commons.R")
require.auto(knitr)
......
......@@ -18,9 +18,9 @@ opts <- docopt(doc, commandArgs(TRUE)) ## does not work when spining
#opts <- docopt(doc, "--overlay_expr_data ../ctrl_fc_expr_filtered.txt geneClusters.RData" )
#opts <- docopt(doc, "--overlay_expr_data ../ctrl_fc_expr_filtered.txt grpdGoiClusters.RData" )
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/ggplot_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.12/R/bio/diffex_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.12/R/bio/diffex_commons.R")
require.auto(knitr)
......
......@@ -15,7 +15,7 @@ sdk install kscript
#
#install.packages(c('ggplot2', 'dplyr'), repos='http://cran.rstudio.com/')
#\
#devtools::source_url('https://raw.githubusercontent.com/holgerbrandl/datautils/v1.26/R/core_commons.R')
#devtools::source_url('https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.26/R/core_commons.R')
#
#loadpack(lubridate)
#loadpack(RPostgreSQL)
......
......@@ -33,8 +33,8 @@
## Note This script is supposed to be knitr::spin'ed
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/ggplot_commons.R")
## can we access variables from the parent spin.R process?
#echo("rscript is ", r_script)
......
......@@ -27,8 +27,8 @@ opts = docopt(doc, commandArgs(TRUE))
# LOAD packages -------------------------------------------------------------------------------
#https://www.bioconductor.org/help/workflows/simpleSingleCell/
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.40/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.45/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.40/R/core_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.45/R/ggplot_commons.R")
devtools::source_url("https://git.mpi-cbg.de/bioinfo/ngs_tools/raw/v6/common/cp_utils.R")
library(knitr)
# require(gridExtra)
......
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