Commit a3d3d85d authored by Holger Brandl's avatar Holger Brandl

adjusted readme for public release

parent c320c318
Copyright 2017 Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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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/
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
```
 
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