-
Notifications
You must be signed in to change notification settings - Fork 3
Panoramic setup
The Panoramic package mainly consists of two Snakemake pipelines, which make use of a large number of tools and libraries. I made every effort to save you the mess of having to install all the required software by using Conda environments, so most of the dependencies will be automatically installed by the pipeline. However, there are a few dependencies you'll have to install before you can run Panoramic.
Please note that panoramic is developed to run on a Unix environment, preferably with access to an HPC cluster.
Conda is a popular package and environment manager. I recommend Miniconda (but Anaconda will work as well). Follow the instructions here to install it. Make sure that it is available for you to run from command line. Verify by running:
$ conda -V
MAKER is the annotation tool used by Panoramic. Unfortunately, there is no available Conda env and installing it is a bit of a mess... Visit their website and follow the instructions there. You'll have to register first. If you have difficulties installing MAKER, check out the discussion group. It's OK if you end up installing MAKER using Environment modules, just make sure that you can run maker from the command line like this:
$ maker -version
Once all dependencies have been installed, you can install Panoramic by following the steps below:
- Clone the repository with current development code:
$ git clone https://github.com/MayroseLab/Panoramic.git - To switch to the latest stable release, use:
$ cd Panoramic
$ git checkout <version>, e.g.$ git checkout v1.0.0 - Create the Panoramic environment:
$ conda env create -f conda_env/snakemake.yml - Activate the environment (do this everytime you want to run Panoramic):
$ conda activate snakemake-panoramic
Before running Panoramic for the first time, you'll need to configure MAKER. This is done by editing the files found under genome_annotation/annotation_templates/annotation/maker_exe.ctl. This file contains paths to various executables. You can either complete them manually, or (assuming MAKER was successfully installed), do the following:
$ cd genome_annotation/annotation_templates/annotation
$ mkdir tmp
$ cd tmp
$ maker -CTL
$ cp maker_exe.ctl ../
$ cd ../
$ rm -rf tmp
In additio you need to set a value for the TMP parameter in the maker_opt.ctl file. This should be a path accessible to all machines running the pipeline, for MAKER to write temporary files.
If you're planning to run Panoramic on an HPC cluster (highly recommended), you'll have to make some configurations. Panoramic was tested on a PBS-Pro queue, but should be able to use any queuing system. To configure for your system, you'll need to make some edits to the qsub script found under Panoramic/util/pbs_qsub_snakemake_wrapper.py. Also see the Cluster Execution section in the Snakemake documentation for more details and examples.
To make sure everything works, it is highly recommended that you first try running the test data set before running your own data.