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 to release a set of production pipelines soon so please stay tuned. However, to view our current documentation please see here
We are currently testing a script to automate the installation with conda. Feel free to give it a go:
# 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>
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.
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.