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