CGAT Flow

We have developed a set of ruffus based pipelines in comparative genomics and NGS analysis. We are working on improving the existing documentation and portability of the code so stay tuned. The current documentation of the code is here

If you just want to use the production version of the code, please try the following steps::

# download installation script:
curl -O https://raw.githubusercontent.com/cgat-developers/cgat-flow/master/install.sh

# then run:
bash install.sh --full-install --install-dir </full/path/to/folder/without/trailing/slash>

# you can also test your installation with:
bash install.sh --test --install-dir </full/path/to/folder/without/trailing/slash>

On the other hand, if you prefer to use the development version of the code, run this instead::

# download installation script:
curl -O https://raw.githubusercontent.com/cgat-developers/cgat-flow/master/install-devel.sh

# see help:
bash install-devel.sh -h

./install-devel.sh
	 --install-repo
 --install-pipeline-dependencies
 --clone-from-repo
 --location </full/path/to/folder/without/trailing/slash>

Both scripts use conda to create the appropriate environments for the code to run.

The installation script will put everything under the specified location. It needs 15 GB of disk space and it takes about 35 minutes to complete. The aim of the script is to provide a portable installation that does not interfere with the existing software. As a result, you will get a conda environment working with CGAT Flow which can be enabled on demand according to your needs.

Configure cluster use

On top of the instructions above, please make sure that you configure the following environment variables::

    # Access to the DRMAA library: https://en.wikipedia.org/wiki/DRMAA
    export DRMAA_LIBRARY_PATH=/<full-path>/libdrmaa.so

    # You can get this value from your configured environment:
    env | grep DRMAA_LIBRARY_PATH

    # or just look for the library:
    find <path-to-DRMS-install-folder> -name "*libdrmaa.so"

    # Also, make sure you have defined temporary folders
    # 1. Local to execution hosts with
    export TMPDIR=/tmp
    # 2. Shared to pipeline working directory
    export SHARED_TMPDIR=/<path-to-network-folder>/scratch

For questions, please open a new issue on GitHub