Skip to content

2. Current Version

Jump to bottom
d-j-e edited this page Sep 7, 2016 · 27 revisions

Obtaining the Current Version of RedDog


The latest version of the pipeline (v1beta.10.3) is available from
https://github.com/katholt/RedDog

Make sure that you obtain the ‘Master’ version, which is always the latest, tested version of the pipeline, and not one of the development branches.

To download the latest version from github onto a cluster:

Change directory (cd) to your directory on the drive where you will keep the new version of the pipeline (_e.g._ cd /full_path_to/drive/of/user/)

Then:
``` module load git git clone https://github.com/katholt/RedDog RedDog_v1b10_3 ```
This command will then create a new folder named 'RedDog_v1b10_3' with the latest version of the pipeline (you can use any name you like for this folder...).

Note: these instructions assume you are running the pipeline on a Unix-based cluster environment. Currently, there are versions of Rubra that support SLURM and Torque systems. RedDog is being developed on a SLURM cluster at [VLSCI] (http://www.vlsci.org.au/).

Reporting a Problem with RedDog:

If you want to report a problem with RedDog, or to suggest a change or improvement, please use the RedDog issues page on Github.

When reporting a bug, be sure to include any relevant error messages, the version of the pipeline being used, and the location of the pipeline and the log files (if not within the pipeline folder).

Note: Errors during a run produced by a job failing to finish due to walltime or memory limits should generally not be reported.

First, try extending the walltime or memory (which ever is applicable) of the stage in question (also take into account other stages that may be affected – see below in [Large Data Sets, Large Read Sets and High Variation] () and restart the pipeline – in most cases the pipeline will then take up where it last left off, redoing the failed jobs with the now extended walltime/memory. If on trying this, the pipe fails, then report the problem. See [Troubleshooting] (https://github.com/katholt/RedDog/wiki/12.-Troubleshooting-a-Pipeline-Run) for more information on what to do if things do go wrong.

RedDog Dependencies:

Python v2.7.5+ https://www.python.org/
Ruffus v2+ http://www.ruffus.org.uk/
Rubra https://github.com/bjpop/rubra
Biopython v1.6+ http://biopython.org/wiki/Main_Page
Bowtie2 v2.2.9 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
BWA v0.6.2 http://bio-bwa.sourceforge.net/
SAMTools v1.1+ http://samtools.sourceforge.net/
ea-utils v1.1.2+ https://code.google.com/p/ea-utils/
FastTree v2.1.8+ http://www.microbesonline.org/fasttree/

The list above does not include any further dependencies required by any of the above packages to run correctly – make sure you carefully follow the instructions for each when installing.

Using RedDog on a Dedicated Server

If you are using RedDog on a non-distributed system, i.e. a dedicated server with no queuing system, there is one change needed before running RedDog, and one that should be considered.

First, the needed change; in the config file, look for:

stageDefaults = {
    "distributed": True,

Change the 'distributed' setting to:

"distributed": False,

The second is the number of jobs to be launched ; in the config file, look for:

pipeline = {
    "logDir": "log",
    "logFile": "pipeline.log",
    "style": "print",
    "procs": 50,

If your server has less than 50 processors available, you should change this to a suitable number. You may also want to keep in mind that certain stages can require up to 4 Gb for processing (more for larger runs).

Previous Home Next

Clone this wiki locally