From 4c51eecddae5c6007c8d8cfdf443963dc414ca97 Mon Sep 17 00:00:00 2001
From: Holger Brandl <holgerbrandl@gmail.com>
Date: Fri, 26 Feb 2016 15:26:28 +0100
Subject: [PATCH] adopted fc dba analysis for new data.
---
chipseq_workflow/chipseq_utils.sh | 6 +++---
dge_workflow/dge_utils.sh | 9 +++++++++
2 files changed, 12 insertions(+), 3 deletions(-)
diff --git a/chipseq_workflow/chipseq_utils.sh b/chipseq_workflow/chipseq_utils.sh
index f414191..588fdfa 100755
--- a/chipseq_workflow/chipseq_utils.sh
+++ b/chipseq_workflow/chipseq_utils.sh
@@ -110,10 +110,10 @@ done
wait
echo '
-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/v1.22/R/core_commons.R")
+devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/ggplot_commons.R")
-libSizes <- read.delim("algn_counts.txt", header=F) %>% set_names(c("library_size", "sample"))
+libSizes <- read_tsv("algn_counts.txt", col_names=F) %>% set_names(c("library_size", "sample"))
libSizes %>% ggplot(aes(sample, library_size)) +
geom_bar(stat="identity") +
ggtitle("algn_counts") +
diff --git a/dge_workflow/dge_utils.sh b/dge_workflow/dge_utils.sh
index a59d843..00272dd 100755
--- a/dge_workflow/dge_utils.sh
+++ b/dge_workflow/dge_utils.sh
@@ -61,6 +61,15 @@ mailme(){
}
export -f mailme
+ziprm(){
+ if [ $# -lt 2 ]; then echo "Usage: ziprm <tarbasename> [<file>]+"; return; fi
+
+ tarName=$(date +'%y%m%d')_"$1".tar.gz; shift
+ tar czf $tarName $@; rm $@;
+}
+export -f ziprm
+
+
## no longer needed because packages are no kept in home
#export R_LIBS=/tmp/r_index ## export to make sure that packages are load from local repository, otherwise sqlite won't work
--
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