Commit d9ff7ae6 authored by Holger Brandl's avatar Holger Brandl

added git tag tracer

parent 4872e96f
......@@ -39,6 +39,9 @@ git diff --exit-code
# and log it
git describe --tags >> ${baseDir}/.used_ngs_tools
## since tags are not pushed by default we need to trigger the push
git push --tags
```
......
##todo merge with create_igv_session.R
docopts...
opts$bamfile
...
bamFile=/home/brandl/mnt/chip-seq_study/ChIPSeq_March_2015/data/alignments_mmfilt/K4M_Oblong_mmf.bam
bamBaseName=$(basename $bamFile .bam)
genomeCoverageBed -d -ibam $bamFile | cut -f3 | sort | uniq -c | trim > ${bamBaseName}.coveragedist.txt
echo '
setwd("/Volumes/albert_chipseq/Naha_analysis/BigWig_Files/Combined_BAMS_20141024")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/R/core_commons.R")
require(ggplot2)
covDist = read.delim("NEC_K27_Combined.remdup.bam.sorted.coveragedist.txt", header=F, sep="")
names(covDist)=c("num_bases","coverage")
covDist %<>% arrange(coverage) %>% mutate(total_cov=sum(coverage), cum_coverage=cumsum(coverage), cum_cov_prop=cum_coverage/total_cov)
covDist %>% ggplot(aes(coverage, cum_cov_prop)) + geom_area()+geom_hline(y=0.80, color="red")
cutoff=0.8
igv_track_range<- subset(covDist,cum_cov_prop >= cutoff)[1,]$coverage
print(igv_track_range)
' | R --vanilla
......@@ -140,9 +140,15 @@ rend.R -e ${NGS_TOOLS}/common/cp_enrichment.R --overlay_expr_data ../plot_score_
########################################################################################################################
### Sync back to project space
## version common tools
(cd ${NGS_TOOLS} && test -n "$project" && git diff --exit-code && git tag "${project}__$(date +'%Y%m%d')") || echo "could not tag current branch"
# and log it
git describe --tags >> ${baseDir}/.used_ngs_tools
## bidirectional sync with project space
## todo define mount path on bioinfo for bidirectional synching
# ~/bin/unison ${baseDir:=error} /net/fileserver-nfs/stornext/snfs3/projects/huttnerlab/Paul/fam72d_transfection_seq -fastcheck -times -perms 0 -batch
# ~/bin/unison ${baseDir:=error} /net/fileserver-nfs/stornext/snfs3/projects/huttnerlab/Paul/fam72d_transfection_seq/data -fastcheck -times -perms 0 -batch
# or use a uni-directional sync
#rsync -avsn --delete ${baseDir} brandl@fileserver:/projects//file/server/path
......
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