BABS-ASF-qualityControl

Obtaining the Files You Need

$ git clone https://github.com/crickbabs/BABS-ASF-qualityControl
$ cd BABS-ASF-qualityControl

Compiling the groovy library

This is just some custom groovy code that needs to be compiled:

$ module load groovy/2.5.4
$ make

Installing the conda environment

If you are from BABS

You don't need to do anything. The pipeline is using a qcpipeline conda environment available in our shared space : /camp/stp/babs/working/software/anaconda/envs. Just be sure that anaconda is properly configured.

$ readlink $HOME/.conda
/camp/stp/babs/working/$USER/.conda

$ readlink $HOME/.condarc
/camp/stp/babs/working/$USER/.condarc

$ cat /camp/stp/babs/working/$USER/.condarc
envs_dirs:
 - ...
 - /camp/stp/babs/working/software/anaconda/envs
 - ...
pkgs_dirs:
 - ...
 - /camp/stp/babs/working/software/anaconda/pkgs
 - ...

$ cat /camp/stp/babs/working/$USER/.conda/environments.txt
...
/camp/stp/babs/working/software/anaconda/envs/qcpipeline
...

If you are not from BABS

First, you need to load Anaconda:

$ module load Anaconda2/5.1.0

Then, you create a new environment which will be named qcpipeline:

$ conda env create --file environment.yml

Compiling two required binaries

After having a qcpipeline conda environment:

$ module load Anaconda2/5.1.0
$ source activate qcpipeline
$ cd scripts/cpp
$ make
$ cd -
$ source deactivate

Configuring the pipeline

You need to specify 3 things:

• species: the binomial nomenclature (Homo sapiens or Mus musculus) (at the moment only human and mouse are supported)
• type: the type of experiment (RNA-Seq or other) (at the moment the pipeline is considering the data either as RNA-Seq or something else)
• directories: a list of directories containing the FASTQ files

Running the pipeline

Change the location of the work directory in the run.sh file, and:

$ sh run.sh

The files will be output the current directory, in a subdirectory named after the project name.