Commit 75f91b8a authored by Holger Brandl's avatar Holger Brandl

bug_fixes

parent 7700e36a
......@@ -3,15 +3,15 @@ Cluster
Use
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
/projects/bioinfo/scripts/ngs_tools/v1.0
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
for stable branch, or
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
/projects/bioinfo/scripts/ngs_tools/dev
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
for current master where changes can be added and are pushed occasionally to
the origin on gitlab
......@@ -21,9 +21,9 @@ Bioinfo
To use the structure from above when working on bioinformatics-srv1 just use
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
/home/brandl/mnt/mack/bioinfo/scripts/ngs_tools/v1.0
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
 
How to create a new version tag
......@@ -32,15 +32,16 @@ How to create a new version tag
1. Create branch:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
cd /Volumes/projects/bioinfo/scripts/ngs_tools/dev
git checkout -b v3.23
git push
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
1. Checkout new branch into ngs\_tools as stable version
1. Checkout new branch into ngs_tools as stable version
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
cd /Volumes/projects/bioinfo/scripts/ngs_tools/
newVersion=v1.1
mkdir $newVersion
......@@ -50,21 +51,19 @@ git checkout ${newVersion}
## prevent from writing
chmod -R -w ../$newVersion
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
 
ToDos
====
- Finish igv\_track\_range.sh
- Finish igv_track_range.sh
- Write igv session xml programatically including adjusted track; render open
session link ( like
http://localhost:60151/load?file=/Users/brandl/Desktop/my\_session.xml) to
http://localhost:60151/load?file=/Users/brandl/Desktop/my_session.xml) to
reports above igv-link tables
- Learn from http://www.bioconductor.org/help/workflows/rnaseqGene/
* distance matrix using Poisson Distance
* pca variance proportions on axis
......@@ -318,7 +318,7 @@ keggPathways <- enrResults %>% filter(ontology=="kegg") %$% ac(ID) %>% unique()
# results='asis'
if(!exists("keggPathways") || nrow(keggPathways)==0){
if(!exists("keggPathways") || length(keggPathways)==0){
cat("No enriched pathways found")
}else{
......@@ -452,9 +452,10 @@ ens2entrez <- quote({
# mart <- biomaRt::useDataset(guess_mart(geneLists$ensembl_gene_id), mart = biomaRt::useMart("ensembl"))
## todo fix this https://support.bioconductor.org/p/74322/
mart <- biomaRt::useDataset(guess_mart(geneLists$ensembl_gene_id), mart = biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org"))
mart <- biomaRt::useDataset("mmusculus_gene_ensembl", mart = biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org"))
biomaRt::getBM(attributes=c('ensembl_gene_id', 'entrezgene', 'external_gene_name'), mart=mart) %>% filter(!is.na(entrezgene))
}) %>% cache_it("ens2entrez") %>% distinct(ensembl_gene_id)
}) %>% cache_it("ens2entrez") %>% distinct_all(ensembl_gene_id)
#unlen(ens2entrez$ensembl_gene_id)
toolTipData <- overlayData %>% left_join(ens2entrez)
......
......@@ -91,7 +91,7 @@ dge_fastqc $(ls *fastq.gz) &
mcdir $baseDir/alignments
star_align.kts ${igenome} $(ls ${baseDir}/lanereps_pooled/*.fastq.gz)
star_align.kts ${igenome} $(ls ${baseDir}/lanereps_pooled/*.fastq.gz) 2>&1 | tee star_algin.log
#dge_bam_correlate . & # part of star_align.kts now
......@@ -121,7 +121,7 @@ mcdir $baseDir/dge_analysis
#echo "
#sample_1, sample_2
#unpolarised,liver_polar_stage3
#" | csvformat -T > contrasts.txt
#" | trim | csvformat -T > contrasts.txt
#
......
......@@ -53,6 +53,12 @@ mcdir(){
export -f mcdir
## remove empty lines in input
## see http://stackoverflow.com/questions/16414410/delete-empty-lines-using-sed
trim(){
cat - | sed '/^\s*$/d'
}
mailme(){
echo "Subject:"$1 "$2" | sendmail -v $(whoami)@mpi-cbg.de > /dev/null ;
}
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment