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

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

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

cd /Volumes/projects/bioinfo/scripts/ngs_tools/
newVersion=v1.1
mkdir $newVersion
cd $newVersion
git clone git-srv1:/local/git/bioinformatics .
git checkout ${newVersion}

## prevent from writing 
chmod -R -w ../$newVersion

ToDos

• 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 reports above igv-link tables

• Learn from http://www.bioconductor.org/help/workflows/rnaseqGene/

  • distance matrix using Poisson Distance
  • pca variance proportions on axis