{"id":4776,"date":"2018-06-29T10:24:06","date_gmt":"2018-06-29T10:24:06","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4776"},"modified":"2018-06-29T10:24:06","modified_gmt":"2018-06-29T10:24:06","slug":"gubbins","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/gubbins\/","title":{"rendered":"Gubbins"},"content":{"rendered":"

Overview<\/h2>\n

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. <\/p>\n

Version 2.3.2 is installed on the CSF. This can use Anaconda Python v5.1.0 (python 3.6.4).<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions on accessing Gubbins on the CSF. The source is released under the GNU GPL v2 license.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load one<\/em> of the following modulefile:<\/p>\n

\r\nmodule load apps\/gcc\/python-packages\/anaconda3-5.1.0\/gubbins\/2.3.2\r\n<\/pre>\n
The modulefile will automatically load the required version of Anaconda modulefile for you.<\/p>\n
Running the application<\/h2>\n
Please do not run Gubbins on the login node. Jobs should be submitted to the compute nodes via batch. <\/p>\n
Ensure that your python script reads the number of cores your job has reserved in the batch system by getting the $NSLOTS<\/code> environment variable. You should then pass this value to the Gubbins python functions to ensure your code only uses that number of cores. <\/p>\n
run_gubbins.py [FASTA alignment]<\/p>\n
Serial batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\nrun_gubbins.py [FASTA alignment]\r\n\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -pe smp.pe 8     # Number of cores to use (2-24)\r\n\r\n# You must ensure your python script reads the $NSLOTS environment variable\r\n# to obtain the correct number of cores to use.\r\n\r\nrun_gubbins.py [FASTA alignment] --threads $NSLOTS\r\n\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n