$ git clone https://github.com/crickbabs/BABS-ASF-qualityControl
$ cd BABS-ASF-qualityControl
This is just some custom groovy code that needs to be compiled:
$ module load groovy/2.5.4
$ make
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
...
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
After having a qcpipeline
conda environment:
$ module load Anaconda2/5.1.0
$ source activate qcpipeline
$ cd scripts/cpp
$ make
$ cd -
$ source deactivate
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
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.