Commit 95672d3d authored by Holger Brandl's avatar Holger Brandl

replaced spin with rendr

parent 160f04a1
#source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.8/R/spinr/spin_utils.sh 2>&1 2>/dev/null) 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/ngs_tools/raw/v10/common/bash_utils.sh 2>&1 2>/dev/null)
## configure paths ## configure paths
...@@ -15,7 +16,7 @@ export PYTHONPATH=/home/brandl/bin/macs2/lib/python2.7/site-packages:$PYTHONPATH ...@@ -15,7 +16,7 @@ export PYTHONPATH=/home/brandl/bin/macs2/lib/python2.7/site-packages:$PYTHONPATH
cs_bowtie_qc(){ cs_bowtie_qc(){
echo ' 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/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.8/R/ggplot_commons.R") devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.8/R/ggplot_commons.R")
...@@ -94,7 +95,7 @@ ggplot(algnSummary, aes(condition, multi_mappers_prop)) + ...@@ -94,7 +95,7 @@ ggplot(algnSummary, aes(condition, multi_mappers_prop)) +
#+ results="asis" #+ results="asis"
cat("<embed src=\"./bc.pdf\" width=\"900px\" height=\"700px\">") cat("<embed src=\"./bc.pdf\" width=\"900px\" height=\"700px\">")
' | spinsnip "bowtie2_qc" EOF
} }
export -f cs_bowtie_qc export -f cs_bowtie_qc
......
...@@ -49,8 +49,8 @@ export PATH=/home/$(whoami)/.local/bin:$PATH ...@@ -49,8 +49,8 @@ export PATH=/home/$(whoami)/.local/bin:$PATH
append2path ${BIO_BIN_BASE}/joblist_v0.7.1 append2path ${BIO_BIN_BASE}/joblist_v0.7.1
## make sure that rend.R is present ## make sure that rend.R is present
source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.46/tools/rendr/rendr_utils.sh 2>&1 2>/dev/null) 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/ngs_tools/raw/v8/common/bash_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)
mcdir(){ mcdir(){
......
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