adjusted readme for public release

LICENSE

+Copyright 2017 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+x
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

-Cluster
-=======
+NGS Tools
+=========
 
-Use
+Created by the Scientific Computing Facility @MPI-CBG
 
-```
-/projects/bioinfo/scripts/ngs_tools/v1.0
-```
-
-for stable branch, or
-
-```
-/projects/bioinfo/scripts/ngs_tools/dev
-```
+Includes tools and workflows for RNA-Seq, ChIP-seq, and gene list comparison and enrichment analysis.
 
-for current master where changes can be added and are pushed occasionally to
-the origin on gitlab
+For questions ask [us](mailto:bioinformatics@mpi-cbg.de)
 
-Bioinfo
-=======
+Feel welcome to use this repo under the termss of our [license](LICENSE).
 
-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 tag it for a project
----------------------------
+How to use?
+-----------
 
+E.g. for RNA-Seq
 ```bash
-# ensure there are no pending changes
-# http://stackoverflow.com/questions/5139290/how-to-check-if-theres-nothing-to-be-committed-in-the-current-branch
-git diff --exit-code
-
-# create the tag for current branch 
-(cd ${NGS_TOOLS} && test -n "$project"   && git diff --exit-code && git tag "${project}__$(date +'%Y%m%d')")  || echo "could not tag current branch"
+git clone git@git.mpi-cbg.de:bioinfo/ngs_tools.git /some/where
 
-# 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
+export NGS_TOOLS=/some/where
+source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
+export PATH=${NGS_TOOLS}/dge_workflow:$PATH
 ```
 
-
-How to create a new version tag
--------------------------------
+Note that the `NGS_TOOLS` variable is required because some of the scripts rely on it for to locate helper scripts.
 
 
-1.  Create branch:
+VCS model
+---------
 
-```
-cd /Volumes/projects/bioinfo/scripts/ngs_tools/dev
-git checkout -b v3.23
-git push
-```
+All changes are applied to `master` branch, and project specific tags are created whenever an analysis was done.
 
-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
-====
+References
+==========
 
--   Learn from http://www.bioconductor.org/help/workflows/rnaseqGene/
-	* distance matrix using Poisson Distance
+-   http://www.bioconductor.org/help/workflows/rnaseqGene/
 

devel_notes.md

+
+How to tag it for a project
+---------------------------
+
+```bash
+# ensure there are no pending changes
+# http://stackoverflow.com/questions/5139290/how-to-check-if-theres-nothing-to-be-committed-in-the-current-branch
+git diff --exit-code
+
+# create the tag for current branch 
+(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
+
+## since tags are not pushed by default we need to trigger the push
+git push --tags
+```
+
+
+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
+```
+
+ 
\ No newline at end of file