https://github.com/dicaso/genairics

GENeric AIRtight omICS pipelines
https://github.com/dicaso/genairics

bioinformatics omics pipelines

Last synced: 6 months ago
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GENeric AIRtight omICS pipelines

• Host: GitHub
• URL: https://github.com/dicaso/genairics
• Owner: dicaso
• License: other
• Created: 2017-12-08T09:32:01.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2020-12-16T13:04:11.000Z (over 5 years ago)
• Last Synced: 2025-09-13T05:34:01.292Z (10 months ago)
• Topics: bioinformatics, omics, pipelines
• Language: Python
• Size: 1.21 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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# GENeric AIRtight omICS pipelines



## Design goals

### generic pipelines

The pipelines here available are mainly developed for my specific

bioinformatics needs and that of my collaborators. They are build up

in a generic way, and some of the functionality in the main genairics

package file might help or inspire you to build your own

pipelines. The core of the pipelines is build with

[luigi](https://luigi.readthedocs.io) and extensions are provided in

this package's initialization file.

### airtight pipelines

The pipelines are build so they can be started with a single,

fool-proof command.  This should allow collaborators, or scientists

wanting to replicate my results, to easily do so. A docker container

is provided with the package so the processing can be started up on

any platform.

### omics pipelines

The pipelines grow organically, as my research needs expand. I aim to

process any kind of data. If you want to use my set of pipelines, but

desire an expansion to make it more omics-like, contact me and we can

see if there are opportunities to collaborate. More generally,

everyone is welcome to leave suggestions in the [issues

section](https://github.com/beukueb/genairics/issues) of the

repository.

## Installation

### genairics package

#### Dependencies

Python 3 has to be installed: see https://www.python.org/downloads/ for instructions.

#### Prepare virtualenvwrapper [optional]

     sudo pip3 install virtualenvwrapper

     echo "export WORKON_HOME=~/Envs" >> ~/.bashrc

     echo "export VIRTUALENVWRAPPER_PYTHON=$(which python3)" >> ~/.bashrc

     . ~/.bashrc

     mkdir -p $WORKON_HOME

     . /usr/local/bin/virtualenvwrapper.sh

     mkvirtualenv -a ~/genairics -i ipython

#### Install

     workon genairics #only when working in virtualenv

     # For stable version:

     pip3 install genairics

     # For latest development version:

     # pip3 install git+https://github.com/dicaso/genairics.git

Start up console with `genairics console` and execute the following line:

    InstallDependencies()

### Get your BASESPACE_API_TOKEN accessToken

Follow the steps 1-5 from this link:

https://help.basespace.illumina.com/articles/tutorials/using-the-python-run-downloader/

	emacs ~/.BASESPACE_API #Store your accessToke here, instead of emacs use any editor you like

	chmod 600 ~/.BASESPACE_API #For security, only rw access for your user

### Prepare your HPC account [for UGent collaborators]

Go to https://www.ugent.be/hpc/en/access/faq/access to apply for access to the HPC.

#### add to your HPC ~/.bashrc =>

    export GAX_RESOURCES=$VSC_DATA_VO/resources

    export GAX_DATADIR=$VSC_DATA_VO_USER/data

    export GAX_RESULTSDIR=$VSC_DATA_VO_USER/results

    export BASESPACE_API_TOKEN= #Set this to your basespace api token

    export PATH=$VSC_DATA_VO/resources/bin:$PATH:~/.local/bin

    if [[ -v SET_LUIGI_FRIENDLY ]]; then module load pandas; unset SET_LUIGI_FRIENDLY; fi

    if [[ -v R_MODULE ]]; then module purge; module load R-bundle-Bioconductor; unset R_MODULE; fi

#### Execute the following commands

    module load pandas

    pip3 install --user --upgrade genairics

    mkdir $VSC_DATA_VO_USER/{data,results}

Rerun the first two of these lines whenever you need to upgrade your genairics version.

## Example run

### Docker

    docker run -v ~/resources:/resources -v ~/data:/data -v ~/results:/results \

	       --env-file ~/.BASESPACE_API beukueb/genairics RNAseq \

	       NSQ_Run240 --genome saccharomyces_cerevisiae

### qsub job

    genairics --job-launcher qsub RNAseq NSQ_Run240

## Epilogue

There comes a point in time when any human just has to develop their

own, fully-fledged computational genomics platform. This is not that

time for me, but it is good to set it as an aim: aiming for the stars,

landing somewhere on the moon. Of course, with help I should be able

cover more distance, so if you like this project and want to help out,

contact me.