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 occassionally to the origin on git-srv1

Bioinfo

To use the structure from above when working on bioinformatics-srv1 just use

/home/brandl/mnt/mack/bioinfo/scripts/ngs_tools/v1.0

Get started with an RNASeq Project

1. use /Volumes/projects/bioinfo/scripts/ngs_tools/dev/misc/new_project_template.sh to setup project directories

2. copy /Volumes/projects/bioinfo/scripts/ngs_tools/dev/dge_workflow/dge_master_template.sh to scripts directory

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

ToDo

• mcdir sourced in?

• use STAR for mapping

• split cuffdiff report into individual tools

• Use featureCounts and DesSeq2 for differential expression analysisf

• Finish igv_track_range.sh

• Better peak report bioinfo_templates/chipseq_workflow/peak_report.R

• Write igv session xml programmatically 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

• Use proper redmine tracker to evolve the shared codebase